Noam Chomsky was among 20 academics who privately lobbied Professor Stephen Hawking to boycott a major Israeli conference, it has emerged.

Chomsky, a US professor and well-known supporter of the Palestinian cause, joined British academics from the universities of Cambridge, London, Leeds, Southampton, Warwick, Newcastle, York and the Open University to tell Hawking they were "surprised and deeply disappointed" that he had accepted the invitation to speak at next month's presidential conference in Jerusalem, which will chaired by Shimon Peres and attended by Tony Blair and Bill Clinton.

Hawking pulled out this week in protest at Israel's treatment of Palestinians, in the wake of receiving the letter and soundings from Palestinian colleagues. The 71-year-old theoretical physicist's decision has been warmly welcomed by Palestinian academics, with one describing it as "of cosmic proportions", but was attacked in Israel.

On Friday the liberal academic David Newman, dean of the faculty of humanities and social sciences at Ben Gurion University in Israel, warned that an academic boycott "just destroys one of the very few spaces left where Israelis and Palestinians actually do come together".

Chomsky, who has backed "boycott and divestment of firms that are carrying out operations in the occupied territories", agreed to add his considerable weight to the pressure on Hawking after email correspondence with the British Committee for the Universities of Palestine campaign group (Bricup), said its chair, Jonathan Rosenhead.

The letter to Hawking declared: "Israel systematically discriminates against the Palestinians who make up 20% of its population in ways that would be illegal in Britain", its treatment of the people of Gaza amounts to "collective punishment", the construction of Jewish settlements breaches the Geneva convention and "Israel places multiple roadblocks, physical, financial and legal, in the way of higher education, both for its own Palestinian citizens and those under occupation".

The letter continued: "Israel has a name for the promotion of its cultural and scientific standing: 'Brand Israel'. This is a deliberate policy of camouflaging its oppressive acts behind a cultured veneer."

Professor Malcolm Levitt, a fellow of the Royal Society and an expert in magnetic resonance at Southampton University, who signed the letter, said: "Israel has a totally explicit policy of making life impossible for the non-Jewish population and I find it totally unacceptable. As a scientist, the tool I have available to prevent the normalisation of that situation is boycott. It is a tough choice because Israel is full of brilliant scientists and they are our colleagues."

Bricup is now to call on Lord Skidelsky, a leading economic historian, to refuse his invitation to speak at the conference. Skidelsky, emeritus professor of political economy at the University of Warwick and a crossbench peer, declined to comment and is understood to still be planning to attend.

News of Chomsky's role in what has been considered the coup of Hawking's decision for the movement came amid growing signs in UK academia of interest in supporting boycotts of Israel. At its annual congress beginning on 29 May, the University and College Union will urge its 120,000 members to consider rethinking links with Israeli academic institutions. Teachers and lecturers will be asked to "consider the appropriateness of Israeli institutional associations", according to a draft motion.

"It is brave of Hawking for the straightforward reason that someone who has his prominence will be targeted for vilification," said Tom Hickey, a member of the UCU's executive committee who put forward the draft motion. "If he can do that then all of us should think of doing it. This isn't about targeting Israeli scholars but targeting the institutions."

Pro-boycott academics believe action by scientists is particularly effective in opposing Israel's treatment of Palestinians because the country's strength in science and technology is a key driver of the economy, and they claim the research capabilities of Israeli academic institutions have been deployed in support of advanced programmes such as the development of drone aircraft.

On Friday the fallout from Hawking's decision continued to be felt. "It is one of the starkest indicators yet that the tide is changing in the western mainstream against Israel's occupation, colonisation and apartheid, and that the Boycott Divestment and Sanctions movement is fast reaching its South Africa moment of maturity and impact," said Omar Barghouti, a Palestinian human rights activist and founding member of the BDS.

Others warned it would damage Israeli-Palestinian relations. "There are certain areas that are above political boycotts whatever your political positions are," said Newman. "Scientific co-operation is one of those particularly when you think of the wider benefits of science on the whole. In this context, universities are among the few spaces in Israel-Palestine where, even in these difficult times, there is some sort of dialogue and co-operation."

The British author Ian McEwan, who was criticised two years ago when he visited Israel to accept the Jerusalem Prize, said: "My feeling [in 2011] was that I wished to engage with the best elements of Israeli society and I don't want to isolate those people," he said.

He said there were dozens of countries "whose governments we might loathe or disapprove of" but "Israel-Palestine has become sort of tribal and a touchstone for a certain portion of the intellectual classes. I say this in the context of thinking it is profoundly wrong of the Israeli government not to be pursuing more actively and positively and creatively a solution with the Palestinians. That's why I think one wants to go to these places to make the point. Turning away will not produce any result."

Samia Botmeh, director of the centre for development studies at Birzeit University in the West Bank, and a member of the Palestinian Campaign for the Academic and Cultural Boycott of Israel's steering committee, said Hawking's decision had significantly boosted the boycott movement locally and internationally, but denied there had been a "huge, orchestrated campaign" to persuade him. "It will be easier now for other academics who have been supportive of Palestinian rights but were reluctant to act on their support," she said.

• This article was amended on 13 May 2013. The original described Lord Skidelsky as a Tory peer. He is a crossbench peer.