Mr Trup said: "I felt uncomfortable when a student brought up the issue of rising antisemitism in Europe and there was a groan from many. When people mention other types of oppression such as sexism, racism or homophobia, they are listened to respectfully; when a student brings up antisemitism, it felt like people didn't take it seriously."
Mr Trup received 10 complaints following the meeting from students who said they had felt intimidated. Jewish students also reported being told they could not be trusted to represent their colleges at the debate because "as Jews they may have had a conflict of interest".
Meanwhile the Cambridge Union Society has passed a motion that Israel is a "rogue state". 51 per cent voted in favour, 19 per cent against and 30 per cent abstained.
Board of Deputies president, Vivian Wineman, spoke against the motion with Yachad director, Hannah Weisfeld, and Davis Lewin, deputy director of the Henry Jackson Society think-tank.
Mr Lewin was booed as he attacked anti-Zionist academic Norman Finkelstein, who was backing the motion.
The 200-year-old society is independent but many Cambridge University students are members.
History student Alex Davis said: "The debate revealed an uncomfortable truth: pro-Israel supporters are losing the argument on campus. Many Cambridge students felt frustrated by the inability of some of the speakers to argue effectively in defence of Israel."
● Pro-Israel lawyers have asked Paul Webley, the director of the School of Oriental and African Studies, to ensure that Israelis are not discriminated against in the wake of Soas's student union's "referendum" on boycotting Israel.
UK Lawyers for Israel also urged that staff buying products for Soas should be told not to boycott Israeli goods.
