A recommendation by Turkey's Education National Congress has drawn angry reactions from the country's Islamic community, who fear a back-door attempt to prevent religiously trained pupils from entering the university system.
The advisory congress, organised by the ministry of education every five years, called for the closure of religious training schools and their incorporation into the general education system.
Fehmi Koru, a former presidential adviser and columnist for the Islamic newspaper Zaman, reacted angrily to the decision: "Those who support the move intend to withhold from graduates of these schools a right they have enjoyed for nearly 20 years - the right to enrol in a faculty if they get the right mark in the entrance exam."
Religious schools in Turkey are run by the state, but paid for by the religious community mainly for the training of Imams. Pupils were originally only allowed to attend special religious universities or study theology at mainstream universities. But a ruling by the supreme court gave them the right to study any subject.
In the past ten years greater numbers have entered mainstream universities, causing concern that the secular nature of the state is being threatened. Turkey has been a strict secular state since the formation of the republic in 1923.
But the expansion of Imam schools was part of a policy by the leaders of Turkey's military coup in 1980 to encourage Islam as a means of undermining support of left-wing parties.
The policy was continued by the late President Turgot Ozel in a bid to secure conservative votes in election campaigns, a strategy which is still followed today by both centre-right political parties.
Turkan Saylan, a lecturer at Cappar Medical University, is a founder of the Society of Contemporary Living which campaigns for secular rights in Turkey.
She believes the congress decision is a positive step. "This is an important step towards a more contemporary education system, religion and politics should have no place in our education system. The growth in numbers of religious students is changing everything."
Assistant professor Istar Gozaydin of Istanbul's Maramara University believes such fears are well-founded. "The growth in students from Imam schools has been dramatic and has changed the whole composition of the university intake in various faculties.
"In Istanbul's law faculty alone over 40 per cent of the students are from Imam schools. Obviously after they complete their studies they will become the country's lawyers, judges and top civil servants. It will change the fabric of the country."
As Turkey's Islamic parties edge closer to power, the ministry has not made a decision on whether to implement the policy, but Dr Gozaydin is sceptical. "Even if the ministry resists pressure from the Islamic community and adopts the reforms it will still have to push the reform through parliament and with the present state of the parliament that is impossible, the Islamists are simply too powerful."
The Islamic Refah Party, the largest party in parliament, has condemned the reform. Abdullah Gul, general secretary, said: "The people who attended the congress do not represent the people, they're only interested in their left-wing agenda which wants to ignore and exclude religion in our society. The decision isn't binding and has to come before parliament, where we will oppose it."