A union leader has denied that her organisation's Jewish members were subjected to a "hostile environment" during years of debate over a proposed academic boycott of Israel.

Sally Hunt, University and College Union general secretary, said the organisation did not tolerate antisemitism, but admitted that at times it had "fallen short".

Ms Hunt was giving evidence in defence of her union at the employment tribunal brought by maths lecturer Ronnie Fraser, who claims the union has not done enough to challenge antisemitism.

Opening his cross-examination of Ms Hunt at London's Central Employment Tribunal last Friday, Mr Fraser's lawyer Anthony Julius, of Mishcon de Reya, asked whether the union had taken seriously the allegations that it was "institutionally antisemitic".

"It is Mr Fraser's case that the answer to that question is no," said Mr Julius.

Mr Julius and Ms Hunt repeatedly clashed during continued cross-examination on Monday. In one exchange Mr Julius alleged that the union "has zero tolerance for racism of colour, but a great deal of tolerance for antisemitic racism", a point Ms Hunt denied.

Asked how she would respond if someone said "If you want to know the truth about Jews, read Mein Kampf," Ms Hunt responded: "It could mean you could learn about the Holocaust." Was it antisemitism, she was asked? When she said it depended on the context, Mr Julius retorted: "Do you accept from me that your resistance to accepting plainly antisemitic material is tactical in this case?" She denied that charge.

Questioning focused on UCU's handling of a complaint from Mr Fraser about the actions of a Glasgow University UCU member, Keith Hammond.

Mr Fraser had complained that Mr Hammond had made antisemitic remarks in a post on the UCU activists' online forum in January 2010.

The UCU investigation ruled that the post – which included the suggestion that then-Prime Minister Gordon Brown was "Israel's man in Number Ten", and another which implied that "Zionists" were responsible for university department closures – were not antisemitic.

Mr Julius asked: "Do you think Mr Fraser would be entitled to infer from this decision that the union was not taking antisemitism seriously?" Ms Hunt replied: "I think he would."

But she argued that Mr Fraser could not be considered "an ordinary Jewish member of the union" because he had spent so much time working on the issues of anti-Zionism, antisemitism and UCU's proposed boycott of Israel.

The tribunal heard that the UCU had sought a legal opinion from Lord Lester on the issue of whether debates singling out Israel would breach discrimination legislation.

Ms Hunt said: "Lord Lester was very clear that individuals could debate the policies of Israel in a way they did not debate other countries. Everything that we did was in the context of the Lord Lester advice."

However she acknowledged that only a "very limited number of people" at the UCU had seen the advice.

Mr Julius said the EUMC definition of antisemitism that the union rejected last year had been used successfully by other organisations. The National Union of Students, he said, had used it to bar speakers with a history of antisemitism from appearing on campuses.

Yet UCU activist Sue Blackwell had claimed the definition was "not fit for purpose", he said. Mr Julius said it was a matter of regret that Ms Blackwell had not been called by the union to give evidence to the tribunal.

He said Ms Blackwell had treated Mr Fraser as a "figure of fun" after he spoke during the congress debate last year at which the definition was rejected.

"Absolutely not," said Ms Hunt. "Jewish members spoke on both sides of the debate. Congress listened very quietly to what Ronnie Fraser had to say. I thought it was a brave speech to have made."

On Monday, John Mann MP told the tribunal that the union had refused to accept the report of the 2006 All-Party Parliamentary Inquiry into Antisemitism. Cross-examined by the UCU's lawyer Antony White QC, Mr Mann said he had been "gobsmacked" when union representatives, including Ms Hunt, had refused to discuss antisemitism during a meeting in Parliament in 2006.

"The disappointment with UCU is that they were not even properly engaged," he said.

The tribunal heard its final evidence, after two and a half weeks, on Wednesday. The panel is unlikely to deliver its judgment before the end of the year.