The Los Angeles-based Simon Wiesenthal Center said the South African archbishop's call was "unjust and a distortion of the truth".
The organisation was responding to an article which appeared in the International Herald Tribune newspaper in which the archbishop compared Israel's actions with those of the apartheid regime.
The Nobel laureate said that Israel's policies should be opposed and that divestment from Israel was "the first, though certainly not the only, necessary move in that direction".
Archbishop Tutu led a campaign encouraging divestment from South Africa under the former white-led government.
'Siding with aggressors'
Rabbi Marvin Hier, dean and founder of the Simon Wiesenthal Center, said the archbishop was wrong to encourage anti-Israel activity.
"Rather than urge American universities to divest from the Middle East's only democracy, Tutu should be urging Muslim religious and political leaders to unequivocally condemn the terrorist organisations whose only aim is the total destruction of the State of Israel," he said.
"What is most hurtful is rather than cry out on behalf of the innocent victims of terror, Tutu aligns himself with those who have refused to stop it."
Palestinian restrictions
In his article, the archbishop drew parallels between South African apartheid and Israel's actions in the West Bank and Gaza.
"Yesterday's township dwellers can tell you about today's life in the occupied territories," Tutu wrote.
"More than an emergency is required to get to a hospital; less than a crime earns a trip to jail," he added.
Rabbi Hier said Archbishop Tutu's comparison was a distortion of the truth.
"In South Africa, a minority controlled and denied the rights of the majority. In Israel, all citizens, including Israeli Arabs, have equal rights under the law."
He said: "If there are security checkpoints in Israel, it is because there have been 70 suicide attacks that have murdered more than 260 men, women and children.
"If ambulances are checked, it is because the Palestinians have used them to conceal terrorists and weapons in their attacks."
Archbishop Tutu noted that similarities between South African apartheid and Israel's policies were not exact, acknowledging that Israel "is certainly more democratic than most of its neighbours".