Although the head-to-toe covering known locally as the niqab is "not a phenomenon" among his teachers, Gaber Nassar told The Associated Press that he wants to "cure the disease" before it becomes one.
Islamic clerics and students have denounced the move as discriminatory, but Nassar said he has the backing of the Grand Mufti, Egypt's top religious authority.
The niqab, Nassar said, is especially problematic in language courses, where the cloth barrier of the veil hinders student-teacher communications producing low grades and graduates incapable of enunciation.
However the number of women wearing the full niqab veil has increased dramatically in the past 10-20 years.
In 2009, Cairo University had banned both students and staff from wearing the niqab on campus or in the university's dorms. The ban was later overturned by a Cairo court following a lawsuit filed by a professor.
"That was unconstitutional because it said all of the university, we are saying now only the lecture halls," Nassar said, daring anyone to challenge his decree in court. "We are not banning the niqab, we are just regulating it.