Malaysia's Government has accused its religious schools of teaching hate, not religion, and has stopped their state subsidy.
More than 125,000 children in Malaysia receive an Islamic education in such institutions.
Education Minister Musa Mohamad has said the schools could stoke Islamic extremism.
Are religious schools breeding young militants?
"There is enough evidence for us to believe that the private religious schools have the tendency to promote teaching in religious doctrines rather than in religious education, a doctrine that may not be acceptable to a government that is practising democracy," he said.
The Prime Minister, Dr Mahathir Mohamad, has gone further, accusing them of teaching hate.
Indeed, some of the alleged Islamic militants recently arrested in Malaysia have been linked to such schools.
The government has stopped giving any subsidy, and urged parents to send children elsewhere.
But are these schools, also known as madrasas, a hotbed of militants?
Political scientist and commentator Farish Noor said he did not think so.
"I personally haven't come across any cases of madrasas training militants in any of the places I have visited in Malaysia or Indonesia," he said.
"However, when one looks at the syllabus and the sort of texts that are being taught there, I think it is hard to deny that generally the approach to Islam tends to be a very conservative one, and that, for me, is a greater source of concern to me in the long run," he added.
To look at the children, all turned out in neat white and green uniforms at this people's religious primary school in the state of Selangor, charges of extremism are hard to believe.
Mohamad Zulkainan and his friends go to a mainstream school for half the day and then come here.
I asked him why he liked coming to a religious school.
"Because it has good teachers," he said.
Parent Abdul Rahman Jalil explained why he sent his children to the school.
"If they are able to live up to that Islamic expectation the knowledge will make them a better person, there will be a greater sense of morality, there will be a greater fear of doing wrong," he said.
Many suspect that the government's real fear is that religious schools breed supporters for the Islamist opposition
But for many children who attend religious schools full-time, the government contends that their non-religious curriculum is often so poor as to leave them virtually unemployable.
Kamaruddin Sohani, an activist in the main opposition Islamist party Pas who sits on the school's committee, argued that education does not have to determine career.
"This country is being managed by a doctor [Dr Mahathir]. He is not supposed to be managing the country, he is supposed to be a doctor," he said.
But it is not just about employability. Malaysia is a multi-religious, multi-racial society. The children sent to Islamic religious schools are largely ethnic Malays. Some observers worry that the students do not mix with children of other races and religions.
Abdul Rahman said it was politics, not education, that was causing Malaysia's races to drift apart.
Malaysia is predominantly Muslim, but remains under secular rule
"There is no conflict in my children - I encourage them to have Chinese friends and Indian friends and they do come over to the house.
"But it is the political structure of this nation. Our political structure is ethnic based, so there's the pursuit of ethnic interests, and when you pursue that of course you're going to go separate ways," he said.
Other Muslims, like Mariam Abdul, do not favour religious schools. She said her neighbour's children who attend one are far more cut off, socially and academically, than her own.
"My children, they are very modern type one, they can go out here and there, but her children - no they can't. So comparing my children and her children, my children are more advanced than hers.
"In that school they cannot do this, they cannot do that - they have to pray and all that. My children do pray, but it is not by force," she said.
She said her neighbours' children only mixed with their own group, and not with other races.
Farish Noor says that he once asked a successful Malay businessman why he had chosen to send all his children to religious schools.
"He believed that in the future the Islamic opposition party in Malaysia would come to power, and so the choice of sending the kids to madrasas was a rational one," he said.
Many suspect that the government's real fear is that religious schools breed supporters for the Islamist opposition.
Dr Mahathir's party knows it must keep its core Malay Muslim vote if it is to maintain its 45-year grip on power.
It remains to be seen whether the attempt to sideline the schools will stem the rise of religious conservatism in Malaysia, or merely cost the government votes when the country next goes to the polls.