Subjects of criticism
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Palestinian refugees are defined by the UN as Arabs who lived in Palestine for at least two years prior to 1948 and their descendants, and who fled or were expelled from their homes during and after the 1948 Palestine War.
The causes and responsibilities of the exodus are a matter of controversy among historians and commentators of the conflict. Whereas historians now agree on most of the events of that period, there remains disagreement as to whether the exodus was the result of a plan designed before or during the war by Zionist leaders or was an unintended consequence of the war.
Significant international pressure was placed on both sides during the 1949 Lausanne Conference to resolve the refugee crisis. The parties signed a joint protocol on the framework for a comprehensive peace, which included territories, refugees, and Jerusalem, in which Israel agreed "in principle" to allow the return of all of the Palestinian refugees. According to New Historian Ilan Pappe, this Israeli agreement was made under pressure from the United States, and because the Israelis wanted United Nations membership, which required Israeli agreement to allow the return of all refugees. Once Israel was admitted to the UN, it retreated from the protocol it had signed because it was completely satisfied with the status quo and saw no need to make any concessions with regard to the refugees or on boundary questions. This led to significant and sustained international criticism.
Allegations of ethnic cleansing
"New Historian" Ilan Pappe argued in The Ethnic Cleansing of Palestine that Israel's policy between 1947 and 1949, when "over 400 Palestinian villages were deliberately destroyed, civilians were massacred, and around a million men, women, and children were expelled from their homes at gunpoint" is best described as ethnic cleansing. However, Pappe's work has been subject to significant criticism and allegations of fabrication by other historians.
For example, Israeli historian Benny Morris called Pappe "At best... one of the world’s sloppiest historians; at worst, one of the most dishonest." When asked about the 1948 Palestinian exodus from Lydda and Ramle, he responded "There are circumstances in history that justify ethnic cleansing. I know that this term is completely negative in the discourse of the 21st century, but when the choice is between ethnic cleansing and genocide - the annihilation of your people - I prefer ethnic cleansing. [...] There was no choice but to expel that population. It was necessary to cleanse the hinterland and cleanse the border areas and cleanse the main roads. It was necessary to cleanse the villages from which our convoys and our settlements were fired on." He also added in 2008, that "There was no Zionist "plan" or blanket policy of evicting the Arab population, or of "ethnic cleansing". Plan Dalet (Plan D), of 10 March 1948 ... was the master plan ... to counter the expected pan-Arab assault on the emergent Jewish state".
Occupation and annexation of neighboring territories
The territories occupied by Israel from Egypt, Jordan, and Syria after the Six-Day War of 1967 have been designated as occupied territory by the United Nations and many other international organisations, governments and others. They consist of the West Bank and much of the Golan Heights. From the Six-Day War until 1982, the Sinai Peninsula was occupied by Israel, but it was returned to Egypt in the Egypt–Israel Peace Treaty. The Gaza Strip was also occupied by Israel until its unilateral disengagement. UN Security Council resolution 242, emphasized "the inadmissibility of the acquisition of territory by war," setting the stage for controversy on the legal status of areas captured in 1967, and in 1948. There are two interpretations of international law on this matter:
The Israeli position:
- The wars in 1956 and 1967 were waged by Israel to ensure the state's survival. As most hostilities were initiated by the Arab side, Israel had to fight and win these wars in order to ensure the state's sovereignty and safety. Territories captured in the course of those wars are therefore legitimately under Israeli administration for both security reasons and to deter hostile states from belligerence.
- In the absence of peace treaties between all the parties at war, Israel has under all circumstances the right to maintain control of the captured territories. Their ultimate disposition should be a result of peace treaties, and not a condition for them. Even so, Israel asserts that:
- The 1956 war was caused by a pattern of Egyptian belligerence against Israel, culminating with the nationalization of the Suez Canal and the blockage of the canal for Israeli traffic in violation of the Convention of Constantinople and other relevant treaties, in their view a clear casus belli (i.e., an act justifying war)
- The 1967 war was similarly caused by the closing of the Straits of Tiran, the rejection of UN forces in the Sinai desert, and the redeployment of Egyptian forces. Jordan and Syria entered the war in spite of Israeli efforts to keep these frontiers peaceful.
- The 1973 war was a surprise attack against Israel by Syria and Egypt.
The Arab position:
- The 1956 war was a result of a conspiracy between France, the United Kingdom and Israel in violation of Egypt's sovereignty. Egypt claimed several legal justifications for refusing Israel use of the Suez Canal, including the right of self-defence.
- The war in 1967 was an unprovoked act of aggression aimed at expanding the boundaries of Israel, and the territories captured during this war are illegally occupied.
- As a result, the territories must be ceded in order for peace to be achieved.
Israel's annexation of East Jerusalem and the Golan Heights in 1980-1 by the Jerusalem Law and the Golan Heights Law has not been recognised by any other country. The Palestinian Authority, the EU, and the UN Security Council consider East Jerusalem to be part of the West Bank, a position disputed by Israel. International bodies such as the United Nations have condemned the Jerusalem Law as a violation of the Fourth Geneva Convention and therefore hold that the establishment of the city as Israel's capital is against international law. Consequently, countries have established embassies to Israel's government outside of Jerusalem.
Israel unilaterally disengaged from Gaza in September 2005, and declared itself no longer to be in occupation of the Strip. This has been contested by the UN, which though not declaring Gaza "occupied" under the legal definition, has referred to Gaza under the nomenclature of "Occupied Palestinian Territories". Some groups do assert that Gaza is legally occupied.
Alleged lack of democracy
Despite the fact that Israeli security legislation for Palestinian territories does not state that military law applies only to Arab residents of the territories, and not to Jews or to Israeli citizens. Israeli citizens are governed by Israeli law whereas Palestinians are governed by military law.
Some Israeli individuals such as Avraham Burg, Ilan Pappé, Gershom Gorenberg, David Remnick, Oren Yiftachel, and Miko Peled and organisations as Human Rights Watch, B'tselem, Peace Now and others have questioned Israel's status as a democracy. These questions focus on the lack of democracy in the Israeli-occupied territories, not Israel proper. Such criticisms are based on the belief that both Israeli citizens in settlements and Palestinians should be given the right to suffrage, considering the Palestinians are effectively under Israeli authority and thus should benefit from it. They share a concern that the occupation of the territories is not temporary, given the over forty-five year duration and the large and the permanent nature of the Israeli settlements.
The participating High Contracting Parties to the Fourth Geneva Convention, numerous UN resolutions, the International Court of Justice and other instances have ruled that Israel's policy of establishing civilian settlements in territories considered occupied, including in East Jerusalem, is illegal. Israel disputes the notion that the West Bank and in particular East Jerusalem are occupied under international law, though this view is dismissed internationally.
Israel's settlement policy has drawn harsh criticism from the United States and the European Union.
Ali Jarbawi called the policy as “one of the only remaining settler-colonial occupations in the world today.”. In his book “Hollow Land: Israel's Architecture of Occupation”, Eyal Weizman describes Israel's policy as a “political system at the heart of this complex and terrifying project of late-modern colonial occupation.”
The international community criticized Israel for 'failing to protect the Palestinian population' from Israeli settler violence.
Human Rights Watch (HRW) has said Israel operates a "two-tier" judicial system in areas of the occupied Palestinian territories it administers, to an effect which provides preferential services, development, and benefits for Israelis living in settlements in the occupied territories while imposing harsh conditions on Palestinians and other non-Israeli citizens. In some cases Israel has acknowledged differential treatment of Palestinians and Israelis, such as having separate roads for both communities and operating checkpoints for Palestinians, asserting that the measures are necessary to protect Israelis from attacks by Palestinian armed groups.
In 2011 the Israeli parliament passed a law criminalizing participation in boycotts of Israeli settlements. The law drew criticism from the EU, the United States and the Anti-Defamation League.
Amnesty International reported that in 2009 hundreds of Palestinians were detained and held incommunicado for extended periods of time by Israel. While most were later released without charge, hundreds were tried before military courts whose procedures often failed to meet international standards for fair trial. According to Amnesty, almost all Palestinian prisoners were held in violation of international humanitarian law, which prohibits the transfer of detainees to the territory of the occupying power (i.e., Israel proper). It claimed that about 300 minors and 550 adults were held without charge or trial for more than a year.
In 2011, UN Secretary-General Ban Ki-Moon said Israel held thousands of Palestinians as prisoners, and called on Israel to release them. Ban said the release of political prisoners would "serve as a significant confidence-building measure" and boost prospects of peace in the region. Also Amnesty International has called on Israel to release political prisoners, saying "all political prisoners held without charge or trial should be tried in fair trials or immediately released". Israel objects to releasing prisoners, many of whom have been convicted by Israeli courts for violent crimes such as murder . However, several prisoner release deals have been conducted by Israel as a gesture in negotiations, many which involved the release of hundreds or more prisoners.
According to Amnesty International, methods of torture used by Israel on Palestinian prisoners include prolonged tying in painful stress positions, sleep deprivation and threats to harm detainees’ families. Beatings and other ill-treatment of detainees are common during and following arrest and during transfer from one location to another.
Treatment of ethnic and religious minorities
Organizations such as Amnesty International, the Association for Civil Rights in Israel (ACRI), the Israeli government-appointed Or Commission, and the United States Department of State have published reports that document racism and discrimination directed towards racial and ethnic groups in Israel.
According to a study commissioned by Israel's Courts administration and Israel Bar Association, Arab Israelis who have been charged with certain types of crime are more likely than their Jewish counterparts to be convicted, and once convicted they are more likely to be sent to prison. The study also found differences in lengths of prison sentences given, with the average prison sentence at nine and a half months for Jews and 14 months for Arabs.
Rights groups have said that anti-discrimination employment laws in Israel are rarely enforced. A coalition of nine Israeli rights groups has opposed a practice under which companies can advertise their policy to hire only Jewish Israelis, and no Arab Israelis. Companies advertising under a "Hebrew labor" banner adhere to a segregated employment philosophy derived from a practice by Jewish immigrants in Palestine in the first half of the 20th century which was meant to strengthen emerging Israeli industry from British and Arab influence.
Stagnating peace process
In February 2011, Netanyahu called German Chancellor Angela Merkel to complain about Germany's vote in favor of a resolution at the United Nations Security Council to declare Israeli settlements to be illegal and she responded "How dare you! You are the one who disappointed us. You haven't made a single step to advance peace." A few days later veteran Israeli diplomat Ilan Baruch resigned saying that Netanyahu's policies were leading to Israel's delegitimization.
Human shield allegations
The IDF acknowledged using the "Neighbor Procedure” or the “Early Warning Procedure”, in which the IDF would encourage a Palestinian acquaintance of a wanted man to try to convince him to surrender. This practice was criticized by some as using "human shields", an allegation the IDF denied, saying that it never forced people into carrying out the Neighbor Procedure; and that Palestinians volunteered to prevent excess loss of life.
Amnesty International and Human Rights Watch are among the groups who made the "human shield" comparison. The Israeli group B'Tselem also made the comparison, saying that "for a long period of time following the outbreak of the second intifada Operation Defensive Shield, in April 2002, the IDF systematically used Palestinian civilians as human shields, forcing them to carry out military actions which threatened their lives". The Neighbor Procedure was outlawed by the Supreme Court of Israel in 2005 but some groups say the IDF continues to use it, although they say the number of instances has dropped sharply.
Possession of weapons of mass destruction
Israel is seen to possess a nuclear arsenal of about 150 weapons, and Israel has been criticised for maintaining nuclear weapons and for not agreeing to a nuclear-free Middle East zone. In September 2009, the IAEA passed a resolution that "expresses concern about the Israeli nuclear capabilities, and calls upon Israel to accede to the NPT and place all its nuclear facilities under comprehensive IAEA safeguards..." 
Israel has signed the Chemical Weapons Convention but not ratified it, citing neighbouring states that have not done so either. Israel is widely believed to have chemical weapons but officials have never directly admitted it, although in 1990 Science Minister Yuval Neeman threatened to retaliate against an Iraqi chemical-weapons strike "with the same merchandise". Israel has not signed the Biological Weapons Convention.
Targeted killings of terrorists
Amnesty International has condemned Israel's policy of assassinations targeting individuals. Israeli officials have admitted that the policy exists and is being pursued, saying it helps prevent acts of terrorism from being committed against Israel. The United States has a very similar policy. Criticism against has been raised also from some on the Israeli left, who say assassination policy is "gangster behavior" unbecoming of a government and is against Israeli law. Israel's Supreme Court has ruled that assassinations are illegal, but leaked documents suggest that Israel's army has ignored the ruling.
Judaization of Jerusalem
The term Judaization of Jerusalem refers to the view that Israel has sought to transform the physical and demographic landscape of Jerusalem to correspond with a vision of a united and fundamentally Jewish Jerusalem under Israeli sovereignty.
The United Nations has criticised Israel's efforts to change the demographic makeup of Jerusalem in several resolutions. All legislative and administrative measures taken by Israel, which have altered or aimed to alter the character, legal status and demographic composition of Jerusalem, are described by the UN as "null and void" and having "no validity whatsoever". Richard Falk, an investigator with the U.N. Human Rights Council, said that Israel's expansion of East Jerusalem settlements and evictions of Palestinian residents can "only be described in its cumulative impact as a form of ethnic cleansing".
In a 2008 report, John Dugard, independent investigator for the United Nations Human Rights Council, cites the Judaization of Jerusalem among many examples of Israeli policies "of colonialism, apartheid or occupation" that create a context in which Palestinian terrorism is "an inevitable consequence".
The Law of Return
Israel has enacted a Law of Return that allows Jews a fast-track to Israeli citizenship. Palestinian refugees cannot apply for Israeli citizenship under the law since they are not Jewish, though they can apply for Israeli citizenship through the conventional channel. The law has drawn criticism from the Cairo Institute for Human Rights Studies which says the law is a "main example of Israeli laws that discriminate against Palestinian Arabs". The American-Arab Anti-Discrimination Committee says the contrast between the Law of Return and Israeli opposition to the right of return of Palestinian refugees exhibits "barefaced racism". More than 1,000 American Jews have backed a campaign entitled “Breaking the Law of Return”, saying the Law of Return creates an ethnically exclusive citizenship, which they see as unjust.
Critics claim that the guaranteed right for Jews to immigrate to Israel is discriminatory to non-Jews and therefore runs counter to the democratic value of equality under the law.
Former Israeli Prime Minister Ehud Barak stated the current Israeli government is “infected by seeds of fascism” and "needs to be brought down." Zionist Union MK Tzipi Livni stated the government was in a state of "crisis — not only of leadership but of ethics.”