The education secretary, Michael Gove, has accused Universities UK of "pandering to extremism" with controversial guidance endorsing the segregation of men and women at campus events, urging it to be withdrawn immediately.

He said the guidance, which has also been branded not permissible by the Equality and Human Rights Commission (EHRC), was a "disgrace".

Speaking to the Daily Mail, Gove said: "We should not pander to extremism. Speakers who insist on segregating audiences should not be indulged by educators. This guidance is wrong and harmful. Universities UK should withdraw it immediately."

On Thursday, Universities UK, which represents more than 130 higher education institutions, said it was seeking a definitive legal view on the issue from the EHRC after its London headquarters were targeted by student protesters this week.

The EHRC said it was involved in redrafting sections in guidance that said that Muslim and other groups were permitted to voluntarily segregate men and women at events. Its chief executive, Mark Hammond, told the Telegraph: "Equality law permits gender segregation in premises that are permanently or temporarily being used for the purposes of an organised religion where its doctrines require it.

"However, in an academic meeting or in a lecture open to the public it is not, in the commission's view, permissible to segregate by gender."

Universities UK has yet to confirm that it is rewriting the guidance. It has also not yet responded to Gove's comments.

It issued the guidance following a series of Islamic events at campuses at which male and female students had been separated.

The document was aimed at covering the legal issues around hosting external speakers, including how to balance the right to free speech against other considerations.

It took the example of an ultra-orthodox religious group invited to speak as part of a wider series of talks on faith, where the speaker requested the audience be segregated by gender. The guidance says that if, for example, women and men were seated separately side by side rather than men at the front and women at the back there would not necessarily be any gender inequality, and voluntary segregation could be permitted.

Universities UK said it had sought an opinion from the senior barrister Fenella Morris QC, which concluded that the advice was "an appropriate foundation for lawful decision-making by universities".

The guidance prompted widespread criticism and protests from students.