On Wednesday, Turkey's top administrative court ordered the suspension of a decree that allows students from religious vocational schools to move to mainstream high schools to take final exams, thus boosting their chances of entering university.
Secularists in Turkey's educational and judicial establishment fear such moves could increase the influence of Islam and erode the strict division between religion and state.
They distrust the ruling AK Party due to its Islamist roots.
Education Minister Huseyin Celik said: "We're going to oppose the [court] decision. We will exhaust the legal process.
"If you ask me how I evaluate the decision, I cannot say I am happy about it. I would like to express my regret ... and to say that in legal terms I am surprised."
The court gave no reason for its decision to suspend the reform.
But the secularist body in charge of Turkish higher education, which had sought the ruling, said the reform would strengthen religious schools at the expense of others.
Erdogan has tried in the past to
relax the restrictions
Graduates of vocational schools, including the religious ones, are not banned from attending university, but they face obstacles in garnering the points required to win a place to study subjects other than their speciality.
Recep Tayyip Erdogan, the prime minister is a graduate from a religious vocational school and has tried in the past to relax the restrictions, but met similar secularist opposition.
The secularists have also thwarted his efforts to relax a ban on women wearing the headscarf at university.
Erdogan's centre-right Justice and Development Party (AKP), which has a big majority in parliament, denies critics' claims that it has an Islamist agenda.
The vast majority of Turkey's 72 million people are Muslims.