Student officers are concerned about the absence of women in traditional Muslim dress on university campuses.
Kathryn Edwards, communications officer at Leeds University, said the shift was of great concern and was thought likely to be a direct outcome of last month's terrorist attacks in America.
"Students seem to be registering and attending lectures as normal but since the start of term, Muslim students are certainly keeping a much lower profile around the students union," she said.
Women's officer Cath Owen said there was widespread anxiety although no racist incidents had been reported. "We are doing all we can to counter Islamophobia," she said.
Talks are being held with university authorities in an effort to reassure students, and support groups are being set up to respond to requests for help.
Miriam Shah, a third-year student at Leeds Metropolitan University, said some female students were no longer wearing the traditional headscarf.
"Some people have said that wearing the headscarf has made them feel as if they were wearing a Nazi swastika because of other people's reactions," Ms Shah said.
At Bradford University, a Muslim Women's Forum exists to support the interests of students. Founder Shazia Parveen, a third-year history and politics student, has not removed her headscarf but had heard of women who had.
Co-founder Sahmeena Ali feared that since the terrorist attacks, the forum's task would be harder. "I feel that much of the good work we have done has been completely destroyed," said Ms Ali, a social work student.
The forum has arranged a series of talks highlighting topics such as Islamophobia.
"Often people don't know how to talk to us about these kind of concerns for fear of offending us. But we wanted to pose openly the question of whether Islam is something to be scared of. There are so many misunderstandings," Ms Ali said.