A London-born academic at Ben-Gurion University of the Negev has refuted allegations that he compared Israel to the Nazi regime after he cited a well-known poem condemning bystanders during the Holocaust in a piece that was heavily critical of Israel.

Professor David Newman was accused by King's College London Professor Efraim Karsh of being anti-Israel and a "pseudo-academic" following an article that he wrote in the Jerusalem Post last month under the headline Speaking out against the threat.

Writing for the think tank, Middle East Forum, Prof Karsh said that BGU had become a "hotbed of anti-Israel propaganda".

Prof Newman, dean of BGU's faculty of Humanities and Social Sciences, who paraphrased Pastor Martin Niemoller's famous 1946 "First they came for…" poem about the Germans, said Israel would do well to acknowledge the message: "When the government denied the sovereign rights of the Palestinians, I remained silent; I was not a Palestinian," he wrote, continuing with the verse to condemn Israel's treatment of "hapless refugees", Arab citizens and human-rights activists.

The article was published as it emerged that Israel's Council for Higher Education had recommended closing the BGU department of Politics and Government, unless it abandoned its "strong emphasis on political activism."

Prof Karsh accused Prof Newman of adopting the "standard "colonialist paradigm" prevalent among academics, which views Zionism and the state of Israel, not as a legitimate expression of national self-determination but as "a colonising and expansionist ideology and movement".

Prof Newman said that he was simply making his concerns for the state of Israeli democracy clear. He said he was a proud citizen of Israel who spent his life promoting it and defending it against boycott attempts.

He said the question was "how much longer these fanatical and extremist, right-wing people… can be allowed to dictate the public discourse, without any suitable response".