The issue has pitted the country’s staunchly secular establishment against the administration of Prime Minister Recip Tayyip Erdogan, whose Justice and Development party has pro-Islamist roots.
It has also highlighted a continuing clash between the reforming agenda of the government and the conservative views of the military – and in the process sent jitters through Turkey’s economy.
"There is quite a difference in the viewpoints of the government and the establishment over what secularism means," said Garanti bank financial analyst Ceyda Pekel. "As a result, there’s always been a danger of this tension increasing."
When Turkey’s powerful General Staff announced a week ago that it was against the education reform, the Turkish Lira tumbled and the stock market dropped.
However, the argument concerns only one article of a law designed primarily to modify the workings of the country’s university system, which is administered by the staunchly secular Higher Education Board (YOK).
The law would change current discrimination against graduates or religious and "technical" high schools in university entrance exams.
The powerful Turkish military
have opposed the education law
"Currently," said Istanbul high school teacher Yesim Tagla, "all students who want to enter university have to take an entrance exam. However, if you have been to a religious training school, or other technical school, your score in that exam is multiplied by a coefficient that is less than one.
"In other words, even if you do well, your result is cut so dramatically that you don’t stand a chance of getting a place."
Religious training schools – known as Imam Hatips – were reclassified as "technical schools" after the military ousted a pro-Islamist government back in 1997.
The schools had been at the centre of confrontation back then between the government and the generals, who argued the schools were producing radical Islamist students.
Seven years later, the government is trying to reverse that decision and allow graduates from religious and technical schools the same chance in university entrance exam as graduates of other secular high schools.
Opponents claim the move is a direct attempt to remove the secularist principles of education, enshrined in the constitution and law.
"This is a law that will change the structure of the education system and that will make it possible for the future generations to get a religious based education," said parliamentary deputy Onur Oymen of the opposition Republican People’s Party.
The military were also behind the opposition, with a statement from the General Staff saying: "Circles and institutions which are undoubtedly loyal to the basic characteristics of the Republic should not be expected to adopt that draft."
"This is a law that will change the structure of the education system and that will make it possible for the future generations to get a religious based education"
Meanwhile, the university rectors – who are appointed by YOK – have also reacted against the new law.
According to Erdogan Tezic, the present chairman of YOK, the AKP does not have the right to interfere with the education system.
"The government’s strong majority in the parliament does not represent a majority among the people," he said.
However, Prime Minister Recep Erdogan, himself a graduate of an Imam-Hatip school, has hit back, accusing opponents of the new legislation of trying to block the democratic process by subverting the authority and will of the parliament.
"Nobody should try to apply pressure on this will," he said earlier this week. "If somebody attempts to do so, they will see the response of the parliament … Social consensus is not a consensus between institutions, but of the nation."
The sense of a growing confrontation hit the economy earlier in the week too, with the Central Bank twice stepping into the foreign exchange market to prop up the falling local currency.
The Lira, which had been trading at 1.3 million to the US dollar only a couple of weeks ago, slid to nearly 1.6 million against the greenback on 10 May.
After the Central Bank intervened, it then stabilised around 1.547 million as the week drew to a close.
However, according to Tosun Terzioglu, the dean of the private Sabanci University, the whole issue has been exaggerated in an effort to attack the government.
Missing the point
"The Imam-Hatip problem is superficial," Tosun claimed. "Of the nearly one million technical high school students there are only 70,000 attending Imam-Hatip schools. We are being made to fear."
"The Imam-Hatip problem is superficial. Of the nearly one million technical high school students there are only 70,000 attending Imam-Hatip schools. We are being made to fear"
Tosun said it is very dubious whether granting religious high school graduates equal access to higher education would undermine the secular state.
"We define this group of 70,000 as one that we should fear extremely and be scared of. Yet, in our university, after a period of three to four months, you cannot distinguish between which high school the students came from."
Despite this, and though having passed its reforms of the higher education system, the AKP still has a tough exam to come, one set by the military and its opponents.
Now, the law goes to the president for final approval, but he will probably veto it returning it to parliament for another debate. There may also be a Constitutional Court challenge if the government persists in pushing the law through.
But there is a worry among many teachers and students that, in this controversy, education will ultimately suffer.
"They argue about secularism and religious schools," said high school student Erdinc Argun from Istanbul, "yet no one seems to be asking what they should do to give us a better education."