Leading civil rights organisations have condemned Harvard Kennedy School’s denial of a position to the former head of Human Rights Watch over the organisation’s criticism of Israel.

The American Civil Liberties Union called the refusal of a fellowship to Kenneth Roth “profoundly troubling”. PEN America, which advocates for freedom of expression, said the move “raises serous questions” about one of the US’s leading schools of government. Roth also received backing from other human rights activists.

But the Kennedy School found support from organisations that have been highly critical of Roth and HRW, particularly over the group’s report two years ago that accused Israel of practising a form of race-based apartheid in the Palestinian occupied territories.

The Harvard Kennedy School’s Carr Center for Human Rights Policy offered Roth a position as a senior fellow shortly after he retired as director of HRW in April after 29 years. But the school’s dean, Douglas Elmendorf, allegedly vetoed the move.

A professor of human rights policy at the Kennedy School, Kathryn Sikkink, told the Nation that Elmendorf said to her that Roth would not be permitted to take up the position because HRW has an “anti-Israel bias” and its former director had written tweets critical of Israel.

Roth told the Guardian that Harvard’s move was a reflection of “how utterly afraid the Kennedy School has become of any criticism of Israel” under pressure from donors and influential supporters within the school of Israel’s rightwing government.

The director of the ACLU, Anthony Romero, urged the Kennedy School “to reverse its decision”.

“If Harvard’s decision was based on HRW’s advocacy under Ken’s leadership, this is profoundly troubling – from both a human rights and an academic freedom standpoint, he said. “Scholars and fellows have to be judged on their merits, not whether they please powerful political interests.”

PEN America also backed Roth.

“It is the role of a human rights defender to call out governments harshly, to take positions that are unpopular in certain quarters and to antagonize those who hold power and authority,” the group said. “There is no suggestion that Roth’s criticisms of Israel are in any way based on racial or religious animus.

“Withholding Roth’s participation in a human rights program due to his own staunch critiques of human rights abuses by governments worldwide raises serious questions about the credibility of the Harvard program itself.”

The Foundation for Individual Rights and Expression, which promotes free speech on college campuses, wrote to Elmendorf saying that the Kennedy School “undermines its laudable commitment to intellectual diversity and free inquiry when it rescinds a fellowship offer based on the candidate’s viewpoint or speech”.

But Harvard found support from organisations that have been highly critical of Roth and HRW over the group’s reports on Israel.

NGO Monitor, a Jerusalem-based organisation that campaigns against humanitarian groups critical of Israeli government policies, accused HRW under Ross’s leadership of seeking to “delegitimize Israel”.

“The dean at Harvard was not fooled by the moral facade granted to Roth and HRW. He recognized Roth’s central contributions to legitimizing antisemitism,” NGO Monitor’s president, Gerald Steinberg, said.

UN Watch, a pro-Israel lobby group, described the Kennedy School’s move as “good news”.

“Ken Roth had a pathological obsession with singling out Israel for differential and discriminatory treatment, disproportionately to shocking degrees, with the apparent aim to portray the Jewish state in a manner that would evoke repulsion and disgust,” it said.

Roth has long been the target of a personalised campaign of abuse, including charges of antisemitism, even though his father was a Jewish refugee from Nazi Germany. He said HRW faced similar attacks on its motives when it released its report titled A Threshold Crossed: Israeli Authorities and the Crimes of Apartheid and Persecution, even though leading Israeli politicians have also “warned that the occupation has become a form apartheid”.

“The irony is that when we issued the report, the Israeli government was at a loss to find anything wrong with it. They fell back on the usual arguments of, ‘you must be antisemitic’. I take that as a … victory because if all they can do is name call, they have nothing substantive to say,” he said.

The Kennedy School did not respond to requests for comment.