Professor Lawrence Krauss said he had been shocked when taking part at a debate hosted by an Islamic group at a leading British university to find that men and women were segregated.
The professor, a leading physicist and prominent atheist, threatened to walk out unless organisers agreed to let men and women sit together, which was eventually agreed - but was then astonished to find himself being accused of intolerance by angry members of the audience.
He said there had been no such problems when he recently took part in a similar debate in Australia.
But he suggested in Britain people were often too polite to object to such practices as well as being cowed by those eager to protest whenever they felt "their cultural norms are not being met".
He said: "People are not only afraid to offend, but afraid to offend a vocal and aggressive group of people.
"There is a segment of the Islamic community that is very vocal about this."
The professor said: "I think the notion that these cultural norms should be carried out within a broader society that not only doesn't share them but that is free and open is a very serious problem."
Authorities at University College London have launched an investigation into the event last Saturday, at which people who attended were separated into men, women and coupled seating areas - with women at the back.
Professor Krauss said he was later told by one woman who attended that she went into the lecture theatre holding hands with a male friend and pretending he was her boyfriend to be able to sit in the mixed section.
Richard Dawkins, the prominent British atheist, has claimed that the university allowed "sexual apartheid" to take place and said "heads should roll".