Delegates at the first conference of the new University and College Union in Bournemouth voted by 158 to 99 for "a comprehensive and consistent boycott" of all Israeli academic institutions, as called for by Palestinian trade unions in response to Israel's "40-year occupation" of Palestinian land.

The union's leadership must now circulate calls from Palestinians for a boycott of Israeli universities to all branches throughout the country.

Tom Hickey, a Brighton University academic and union executive member, who led the move, said: "There will be adverse effects on individuals, but this is not targeting individuals or trying to break contacts with them." The vote reflected "the deep concern people have".

A boycott might involve refusing to work with journals published by Israeli companies or collaborate on research contracts with Israeli academics.

But Sally Hunt, the general secretary of the union, said: "I do not believe a boycott is supported by a majority of [120,000] UCU members, nor do I believe that members see it as a priority for the union."

The boycott was also opposed by the education minister, Bill Rammell. He said: "The UK government fully supports academic freedom and is firmly against any academic boycotts of Israel or Israeli academics. Whilst I appreciate the independence of the UCU, I am very disappointed that the union has decided to pass a motion which encourages its members to consider boycotting Israeli academics and education institutions. I profoundly believe this does nothing to promote the Middle East peace process."

The issue has been hotly debated over the past five years by academics within the Association of University Teachers and the University and College Lecturers' Union, which merged into the UCU last year.

In 2005, a vote for a boycott by the AUT was rejected at a special meeting later that year. Natfhe continued to support boycotts at its conference last year, but the policy was dissolved when it merged to form the UCU very soon afterwards.

Previous attempts at a boycott have caused international outcry, especially in Israel and the US. When the AUT ratified a boycott in February 2005, the story hit the front pages in Europe, North America and Asia. During the ensuing weeks, a delegation of Israeli academics put pressure on the union by touring UK campuses. Twenty one Nobel prizewinners, including Shimon Peres and Elie Wiesel, wrote to the Guardian, stating: "Academic freedom has never been the property of a few and must not be manipulated by them ... mixing science with politics and limiting academic freedom by boycotts is wrong".

In response to yesterday's decision, Ofir Frankel, spokesman for the Advisory Board for Academic Freedom, said: "We see it as discriminatory and counterproductive. It will make British academia look a little less serious."

Jon Benjamin, chief executive of the board of Deputies of British Jews, said: "Now is the time to strengthen the kinds of relationships that will bring all sides of the Israeli/Palestinian conflict together and, in this country, create a better understanding of the complex issues through that engagement. We call upon the union's leadership and all members who are rightly outraged by the decision to work towards a reversal of this policy."