The guidelines backed the separation of men and women if demanded by visiting speakers.
But the advice sparked a huge backlash amid accusations it was sexist and condoned discrimination.
The guidelines were sent to all Scottish universities by the sector body Universities UK.
Last night the body withdrew part of the document, a controversial case study on the issue, in the face of growing anger.
But it still insisted that the legal situation around the issue was "unclear".
Earlier politicians had condemned the idea that audiences attending events at universities should be separated on the basis of their gender.
Downing Street said that David Cameron felt "very strongly" that such a situation would be wrong and should not be allowed to happen. His official spokesman also made clear that the Prime Minister, who was visiting the north-east of England, was prepared to consider a change in the law if necessary.
Conservative cabinet minister Michael Gove also 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." Earlier this week the Scottish Parliament's Education Committee agreed to write to Universities UK and Universities Scotland seeking clarification on the document.
SNP MSP Stewart Maxwell described the advice as flying "in the face of equal rights - to say nothing of common sense".
The Equality and Human Rights Commission said that while the law allows segregation by gender in religious premises it was "not permissible" in an academic meeting or open lecture.
ECHR chief executive Mark Hammond said: "The UUK's guidance accepts that the initial question is whether that segregation is discriminatory and concludes that the imposition of segregated seating in certain circumstances could be permissible.
"The guidance also gives the impression that the right to manifest or express a religious belief should be balanced against the right not to be discriminated against."