The book has been labeled an antisemitic canard by some historians, including Saul S. Friedman, who contends that Jews had a minimal role in the New World slave trade. Henry Louis Gates, Jr., head of the department of Afro-American studies at Harvard University, called the book "the Bible of new anti-Semitism" and added that "the book massively misinterprets the historical record, largely through a process of cunningly selective quotations of often reputable sources".
The book was criticized for being antisemitic and for failing to provide an objective analysis of the role of Jews in the slave trade. Common criticisms were that the book used selective quotes, made "crude use of statistics," and was purposefully trying to exaggerate the role of Jews.
Historian Ralph A. Austen criticized the book, saying that the "distortions are produced almost entirely by selective citation rather than explicit falsehood ... more frequently there are innuendos imbedded in the accounts of Jewish involvement in the slave trade," and "[w]hile we should not ignore the anti-Semitism of The Secret Relationship..., we must recognize the legitimacy of the stated aim of examining fully and directly even the most uncomfortable elements in our [Black and Jewish] common past." Austen acknowledges that the book was the first book on the subject aimed at a non-scholarly audience.
In 1995, the American Historical Association (AHA) issued a statement condemning "any statement alleging that Jews played a disproportionate role in the Atlantic slave trade."
The publication of The Secret Relationship spurred retorts published specifically to refute the thesis of The Secret Relationship:
- 1992 – Harold Brackman, Jew on the Brain: A Public Refutation of the Nation of Islam's The Secret Relationship Between Blacks and Jews. The booklet was published privately by Bill Adler, the former publicist for Public Enemy, after learning that the rapper Ice Cube had endorsed The Secret Relationship. In his foreword, Adler wrote, "I care way too much about black-Jewish relations – and particularly about black-Jewish relations in the rap community – to allow 'The Secret Relationship' to go unchallenged." The booklet's afterword was written by Cornel West. It was republished that same year, minus its original foreword and afterword, as "Farrakhan's Reign of Historical Error: The Secret Relationship Between Blacks & Jews" by the Simon Wiesenthal Center. In 1994, it was republished for a second time under the title "Ministry of Lies: the Truth Behind 'The Secret Relationship Between Blacks and Jews'" by Four Walls Eight Windows.
- 1992 – David Brion Davis, "Jews in the Slave Trade," in Culturefront (Fall 1992) pp 42–45.
- 1993 – Seymour Drescher, "The Role of Jews in the Atlantic Slave Trade," Immigrants and Minorities, 12 (1993), pp 113–125.
- 1993 – Marc Caplan, Jew-Hatred As History: An Analysis of the Nation of Islam's "The Secret Relationship" (Published by the Anti Defamation League).
- 1998 – Eli Faber, Jews, Slaves, and the Slave Trade: Setting the Record Straight, New York University Press.
- 1999 – Saul S. Friedman, Jews and the American Slave Trade, Transaction.
A post-1991 scholar who analyzed the role of Jews in the overall Atlantic slave trade concluded that it was "minimal," and only identified certain regions (such as Brazil and the Caribbean) where the participation was "significant."
Wim Klooster wrote: "In no period did Jews play a leading role as financiers, shipowners, or factors in the Transatlantic or Caribbean slave trades. They possessed far fewer slaves than non-Jews in every British territory in North America and the Caribbean. Even when Jews in a handful of places owned slaves in proportions slightly above their representation among a town's families, such cases do not come close to corroborating the assertions of The Secret Relationship."