An investigation is underway after reports that seating at another university debate was segregated between men and women.
The Guardian claims a sign posted on the door of the event, at Leicester University in February, pointed males and females to separate seating areas.
It follows a similar event at University College London, where atheists Lawrence Kraus and Richard Dawkins hit out at the organisers over the seating policy.
Both events featured Hamza Andreas Tzortzis, of the Islamic Education and Research Academy (IERA).
On Tuesday, IERA spokesman Saleem Chagtai told The Huffington Post UK Leicester University's Islamic Society had organised the debate, saying: "We were not responsible for the seating in any way, shape or form."
He said it was "standard procedure" for people to want to sit separately, but but said this should never be enforced.
"Obviously the word 'segregation' was used, and it's got these cultural connotations, with civil rights and apartheid," Chagtai said.
"But it's not like that at all. Practising men and women like to sit with people of their own sex.
"It's really a bit of a storm in a teacup."
He said he wanted non-Muslims to come to the debates, and enforced segregation would "not be conducive" to this.
A University of Leicester spokesman said: "The Islamic Society did hold a philosophical discussion, Does God Exist?, on 20 February.
"Just over 100 people attended and sat together in the same hall. The choice of where people sat was left to those attending. No enforced segregation took place.
"Where there is a public event and individuals attending wish, by their own free choice, to sit separately in the same hall, then that is a matter for them.
"People were also free to sit alongside each other if they chose to do so. The University will not intervene over their freedom of where to sit.
"To our knowledge, no-one was forced to sit in any particular seat. If there is evidence of enforced segregation that would be a matter over which the University and Union would investigate."
No issues were raised by the students' union in the aftermath of the event, he said, adding: "The University will investigate whether entrances to the hall for this event were segregated by the Society and will ensure there is no recurrence of this.”
Dan Flatt from the University of Leicester Students’ Union said: “The Students’ Union does not believe in enforced segregation. We trust in our Societies ability to conduct their events in accordance with the principles of the Union.”
Human rights campaigner Peter Tatchell told The Guardian: "Gender segregated seating contravenes the equal opportunities and anti-discrimination policies of universities and student unions.
"Students and staff should not be subjected to sexist segregationist policies."
The Islamic Society of the university has been asked to comment.