Bar-Ilan and Haifa university officials said on Monday they did not expect the boycott call by the 40,000-member Association of University Teachers (AUT) to have any immediate effect.
Nonetheless, they said they would fight the decision and called on the worldwide academic community to reject it.
"This is a very unbalanced decision ... basically a shameful decision," said Bar-Ilan's president, Moshe Kaveh. "In academic spheres, one should not interfere between academic activity and research, and political decisions."
The union, which approved the decision at its annual conference on Friday, said the two Israeli universities had undermined Palestinian rights and academic freedom. It said it would soon issue guidance to its members on what the boycott would forbid.
One university was accused of
having links to a settlement
Haifa University Vice President Ada Spitzer said she did not expect the boycott to immediately effect academic collaboration.
"It's more symbolic than actual damage," she said.
Still, she called it "an important symbolic act," since it is the first time an Israeli university has been subject to a boycott.
"They are erecting a barrier to academic freedom," she said.
The British union said it targeted Bar-Ilan University for its links to the College of Judea and Samaria in the illegal West Bank settlement of Ariel.
"They are erecting a barrier to academic freedom"
Haifa University Vice President Ada Spitzer
It accused Haifa University of threatening to fire an Israeli political science lecturer for supporting a student's research into allegations of killings by Israeli troops.
Both universities on Monday said many elements of the allegations were false.
Kaveh said Bar-Ilan helped supervise standards of the college of Ariel, which awards a joint degree with Bar-Ilan, but that the 22-year-old West Bank college was largely autonomous and on the way to full independence.
"We were like an incubator," he said.
Haifa University targeted
Kaveh, a physics lecturer at Cambridge University for 35 years, said he was planning on doing research in Britain this summer and already had been assured by British colleagues that they would not honour the boycott.
Israel's foreign ministry blasted
the British union for hypocrisy
Haifa University officials said they were baffled by the boycott call, saying it was based on an erroneous understanding of a dispute over a 5-year-old master's thesis.
In the thesis, the student claimed he had uncovered evidence that Israeli soldiers massacred 200 Palestinians during the 1948 war for Israel's independence. The university rejected the thesis after investigating the allegations and concluding the student had fabricated or distorted much of his evidence.
The student later apologised to an Israeli court and admitted to falsifying the story after soldiers involved in the case sued him.
However, Ilan Pappe, a Haifa University professor who helped the student, accused the school of suppressing academic freedom and called on colleagues in Britain and the US to boycott the university.
While Haifa faculty members have filed complaints against Pappe, the university said it had never taken any disciplinary action against him and he remained on the faculty.
Both Israeli universitieshave said they are beacons of diversity in Israel, welcoming students and faculty of all religious, political and ethnic backgrounds. Haifa University, for instance, said 20% of its student body were Palestinians with Israeli citizenship.
"We will continue our efforts to further Jewish-Arab reconciliation, despite politically motivated initiatives to muzzle free speech and the academic discourse," the university said in a statement.
In its decision, the British union also asked its executive committee to consider a boycott against the Hebrew University of Jerusalem for allegedly bulldozing Palestinian homes to make way for new buildings. The university was closed for a Jewish holiday on Monday and officials did not return a message seeking comment.
Israel's Foreign Ministry over the weekend accused the British union of hypocrisy - saying Israel is the only Middle East country with complete academic freedom - and urged British academics to distance themselves from the boycott.
In 2002, hundreds of European academics called for a boycott of Israeli universities to protest against the treatment of the Palestinians. The move led to the firing of two Israelis from British publications, and prompted allegations of discrimination and intellectual censorship.