Radha Bhatt has demanded in a legal letter that Universities UK (UUK), which represents all vice-chancellors in the UK, admit that a guidance on segregation it published last November was "unlawful".
UUK's guidance had cited a case study to justify its policy of allowing the "voluntary" separation of men and women for religious purposes.
It was forced to withdraw the case study last month and to review its guidance after Prime Minister David Cameron said he wanted to ban segregation at universities.
"I don't see this as a Muslim issue. Once you allow one religious group to impose its discriminatory values, it's like a slippery slope, and others will follow," she told the Sunday Times.
"Universities are secular, neutral public bodies that perform public functions, and for them to allow others to impose such discriminatory values is really dangerous."
"I feel that religious sensibilities are taking precedence over basic equality laws and universal human rights protocols and I think equality must always trump religious belief. Of course religious belief is important, but equality trumps it," she added.
A UUK spokeswoman said the organisation "has always maintained that enforced gender segregation at university events is wrong. However, where gender segregation is voluntary the law is unclear".
It is working with senior legal counsel and the Equality and Human Rights Commission (EHRC) "to clarify the position for both universities and students".
The EHRC said last month that the type of segregation proposed by UUK was "not permissible" under gender equality laws.