Calls to strip Turkey's higher education authority of its powers have reached the country's parliament, which is debating legislation to give individual universities more autonomy.
The 19th anniversary of the foundation of the higher education authority, Yok, earlier this month was marked by nation-wide student protests. The army set up Yok, which has sweeping powers over the country's universities, when it overthrew the government in 1980.
Yok has since come under increasing fire from across the political spectrum. Turkish president Ahmet Necdet Sezer has attacked the authority's powers to control the appointment of rectors. He argues that the authority's sole duty should be coordination and planning.
Students with ties to religious groups have joined leftwing students in calling for Yok's abolition.
The university teachers' association has said that the authority's president should resign. It said that "the ramification of deficiencies in the way higher education is run is now being felt, and the need to end Yok's powers is greater than ever".
After the 1980 coup, Yok presided over a wide-ranging purge of academics. Its enforcement of powers to impose a ban on female students who follow Islamic tradition and cover their heads with scarves has caused particular anger.
In the most recent protests, hundreds of students across the country were arrested as most of Turkey's main cities saw clashes between students and the police.
At the main campus of Istanbul University, nearly 2,000 police patrolled, backed up by armoured cars, dogs and special anti-riot squads. Everyone entering the vicinity was searched, while heavily armed police cordoned off the area around the entrance to the university.
Despite such policing, thousands of students tried to march to the entrance of the central campus carrying a coffin with the word Yok inscribed on it. Student Sinan Celik said: "We need democracy in universities now - we must end the fascist control of Yok, which has more to do with military rule than democracy."
More than 100 students were arrested by baton-wielding police who broke up the protest. A police spokesman said that the demonstration was illegal. Similar clashes occurred in the capital, Ankara.
Outside the city, 95 students were detained after being stopped at a police road block that was set up to intercept students coming to protest.