Students at religious schools in Turkey are angry at the president's decision to veto a reform that would have abolished a law discriminating against them in university entrance exams.
But President Ahmet Necdet Sezer's intervention was welcomed by many academics who have been engaged in nationwide protests over the past months. Their stance has been backed by the military, which sees itself as guardian of the secular state.
Religious students' entrance exam scores are reduced by 20 per cent to curtail the number of religious students attending university, a measure introduced in 1997 under pressure from the army.
New legislation transferring much of the control of higher education to the government, as well as dissolving the present higher education board, YOK, sought to ease restrictions on the entrance to university of students from the imam hatips (religious schools).
But President Sezer has vetoed the measure saying it undermines the secular state.
Turkey's 536 imam hatips teach religious courses along with the normal curriculum to some 64,500 students.
At Istanbul's Acibadem Iman Hatips 17-year-old Ayse Gul, who was just about to take her university entrance exam, said: "I want to be a doctor, but I have no chance - this is just wrong. Why should I be discriminated against? I am the same as any other student in Turkey."
Student Ahmet Tan added: "There is no justice in Turkey - we are a Muslim country yet they discriminate against students who are studying religion."
While the Government could constitutionally overturn the veto by passing the legislation again in parliament, this would deepen a political crisis that has already led to large falls in the currency and stock market.
Prime Minister Recep Tayyip Erdogan attacked President Sezer in parliament, saying: "Why do we have elections if the Government cannot carry out the will of the people?"
Worryingly for the Government, the parents of imam hatip students are among the strongest supporters of the ruling AK Party, and the Prime Minster is under mounting pressure to push through the reform.
Mr Erdogan has indicated that the struggle for higher education reform is not over. The Government is expected to re-introduce the legislation in the autumn.
Mr Erdogan's own children have avoided the restrictions by studying at US universities.