The ban on Islamic religious dress for students looks set to become a battle of wills between the army and prime minister Mesut Yilmaz with universities trapped in the middle.
The country's university authority, YOK, has instructed rectors that the ban must be enforced. But it has become the focus of a struggle between supporters and opponents of the Islamic movement.
Fears are mounting that the army may intervene. The army sees itself as guardian of the 75-year-old secular state and is adamant the ban should continue.
General Halk Karadayi, the army chief-of-staff, briefed President Suleymain Demeriel last week over what the army sees as the "Islamic threat".
Prime minister Yilmaz also met military officers for talks. Mr Yilmaz's Motherland party, which relies in part on support from Islamic voters, has become more reluctant to enforce measures against Islamic activities.
The leader of one of the opposition parties, Deniz Baykal, claimed that the army was losing confidence in the government and was considering replacing it with an "interim government", but this was denied by sources in the army.
Prime minister Yilmaz, clearly angered by the rumours, has gone on the offensive.
His tough stance was underlined by his announcement that he had called YOK head Kemal Guruz to inform him that any ban on religious dress in universities would be illegal.
"I told him no law bans head-scarves and his decision does not have legal grounds," he said.
Until now rectors were allowed to decide for themselves how to enforce restrictions on dress.
The Islamic Virtue Party moved a motion of no confidence last week in education minister Hikmet Ulugbay, who is one of the strongest supporters of the ban.
Although the motion was defeated, the debate saw angry scenes in parliament, with MPs exchanging insults and almost coming to blows.
The clampdown on dress follows last year's collapse of the first Islamic-led government, which had been accused of threatening the secular state.
Protests by Islamic students had already forced Kemal Alemdaroglu, rector of Istanbul University, to postpone the ban until the start of the next academic year. It was his decision to enforce restrictions on religious dress last month that provoked the controversy.
He has been among the strongest supporters of enforcing restrictions on religious dress.
Earlier this month senior military officials addressed rectors at a meeting of YOK, at which the army called for the ban to be extended to all universities.
The rectors were given a report prepared by YOK on judiciary decisions about dress. These clearly stated it was illegal for students to enter university campuses in religious dress. The report said: "All administrators in the republic of Turkey are obligated to put into effect the requirements of the laws without personal interpretation."
The report took away the personal discretion given to individual rectors over the issue. Most universities had allowed the restrictions to lapse.
Following the meeting Dr Guruz announced that the ban would be extended to all universities. This enraged protesting Islamic students outside, who accused the rectors of being puppets for the army. Students carried placards saying: "Rectors go back to your barracks."
Medical students at the Cerahpasa medical university in Istanbul started a hunger strike. The university still enforces dress restrictions in some departments.