Professor Paul Grayson told the Toronto Star the student in an online sociology class emailed him in September to say he had a problem with participating in a focus group with other students, the class's only in-person requirement.
"One of the main reasons that I have chosen Internet courses to complete my BA [bachelor of arts] is due to my firm religious beliefs," the student wrote. "It will not be possible for me to meet in public with a group of women (the majority of my group) to complete some of these tasks."
Grayson said he forwarded the email to the faculty's dean and the director for the center for human rights. He said he was shocked the administrators sided with the student.
"In order to meet an instance of a religious requirement we have tacitly accepted a negative definition of females," Grayson told the Star. "That's not acceptable."
The newspaper said Wednesday the vice dean's reasoning was that students studying abroad in the same online class were accommodated by allowing them to complete an alternative assignment.
"I think Mr. X must be accommodated in exactly the same way as the distant student has been," the vice dean wrote to Grayson.
Grayson says the two situations are not the same.
"York is a secular university. It is not a Protestant, Catholic, Jewish, or Muslim university," he said. "In our policy documents and (hopefully) in our classes we cling to the secular idea that all should be treated equally, independent of, for example, their religion or sex or race.
"Treating Mr. X equally would mean that, like other students, he is expected to interact with female students in his group."
A university provost told the Star the decision in favor of the student was made after consulting legal counsel, the Ontario Human Rights Code and the university's human rights center.