An academic says he threatened to walk out of a debate hosted by the Islamic Education and Research Academy (iERA) because organisers tried to segregate the audience.
Professor Lawrence Krauss, one of the world's leading atheists, was lined up to debate against Islamic lecturer Hamza Andreas Tzortzis at University College London on Saturday.
Women were reportedly told by organisers to sit separately from men and couples.
Krauss refused to participate in the debate, entitled 'Islam or Atheism: Which Makes More Sense?' until they changed their minds.
He tweeted: "Almost walked out of debate as it ended up segregated + saw 3 kids being ejected for sitting in wrong place. I packed up and they caved in."
Krauss posted a link to a video and account of the row from a woman who said she had been told "women were to sit in the back of the auditorium, while men and couples could file into the front."
Zayd Tutton of the iERA disputed Krauss' account of events.
Speaking to the Huffington Post UK, he said: "There were three sections as agreed with UCL prior to the debate. This was agreed clearly with UCL representatives.
"Muslim women choosing to adhere to orthodox Islamic principles in sitting in their own area had their own section.
"As for those who wanted to sit together, male or female, they had their own section where they freely mixed and sat together from the beginning."
Tutton also said the "3 kids" mentioned by Krauss were in fact two men who forcibly tried to sit in the female section.
He said: "When arguing it was about sitting in any area in the auditorium, they were offered an entirely free aisle in the aforementioned Muslim female section, but insisted that they wanted to sit in between the Muslim females, with a view to offending their religious beliefs.
Krauss's fellow atheist Richard Dawkins joined in the row on Twitter.
The debate continued, but the live twitter stream made no mention of the row over seating that came before.