This is no ordinary reception class. It doesn't start till 6pm, and the children in the classroom at Crown Hills community college, Leicester, will spend the next 90 minutes studying Arabic and prayer. Welcome to Crown Hills madrasa. Ahmed Burani, "five and a half", says he loves coming here five days a week. He particularly likes Arabic. "I know my numbers and colours," he says proudly.

Ahmed is one of 250,000 Muslim children attending roughly 2,000 madrasas in the UK. Children typically attend for up to two hours every night until the age of 14-15. Most madrasas operate out of mosques, but a sizeable number are based in schools or community centres. Some are run informally in private homes. Over a quarter have more than 140 pupils a week. While many make a valuable contribution to society, new research by the Institute for Public Policy Research (IPPR), to be published tomorrow, has found that a significant minority do not provide adequate standards of teaching or child protection.

"Madrasas have the potential to positively influence Muslim children's development, allow pupils to explore and understand their own identity and strengthen community cohesion" the report concludes. "However, this is held back by poor teaching standards and narrow curricula in many madrasas."

Some, it points out, are still using corporal punishment because the law does not prohibit this in "supplementary" schools. Madrasa staff can use "reasonable punishment" as a legal defence for any physical action against children. Physical punishment was banned from mainstream schools in 1987. "Madrasas were sometimes seen to use excessively strict approaches to discipline," the report notes. "In a small number of cases, the discipline used was seen to be detrimental to the welfare of children."

IPPR's survey of 179 madrasas also highlights concerns about how well pupils are kept safe. Supplementary schools are exempt from the requirement on other organisations working with children to conduct CRB (Criminal Records Bureau) checks of staff and volunteers. Although the research reveals that most have a child protection policy and carry out CRB checks on staff, a significant minority do not.

"The current legal situation leaves children without sufficient protection," the authors say. There is "a massive loophole" in safeguarding children in madrasas and other supplementary schools. "All supplementary schools, including faith ones, should be required by law to CRB-check their staff," they say. In addition, the report calls on the government to extend the ban on physical punishment to supplementary schools and for madrasa staff to undergo much more training on how to implement child protection policies.

The report also highlights a lack of adequate teacher training and modern teaching methods. Only 14% of madrasas insist on qualified teacher status for staff. More emphasis is placed on teachers' religious credentials, with 57% of madrasas requiring theological training and three quarters using imams to teach. But 10% of madrasas said there were no minimum qualifications for their teachers whatsoever. The report reveals that most madrasas want better connections with their local communities and are keen to develop closer ties with mainstream schools. To do this, they need more support and encouragement from local authorities, the madrasas say. But researchers found some councils were much more proactive than others, with Bradford, Kirklees and Leicester councils leading the way. Mohammed Patel, coordinator of the safeguarding in madrasas project at the Federation of Muslim Organisations, estimates that there are 85 madrasas in Leicestershire. Of these, 66 have signed up to the safeguarding project, a collaboration between the FMO, Leicester council and the police. "95% of madrasas in our project have CRB-checked all their staff and over the last three years, more than 500 people have taken up the training we provide," he says. As a result, Patel says, none of the 66 madrasas uses corporal punishment. "Forget the smacking, pinching, hitting with a pencil, or making a child stand up or sending them outside the classroom. We say there should be no form of punishment at all in madrasas."

But there's more to do on safeguarding he says. "Not all madrasa teachers have training in special needs and many don't have teaching qualifications." To help, the FMO has teamed up with Uplands primary school, which is to provide madrasa teachers with training in teaching methods and behaviour management.

A "zero tolerance" scheme to protect children was launched in September. Madrasas that sign up must have a child protection policy and staff must be given training. Accredited madrasas will be awarded a certificate and the FMO will go back every year to check progress.

Crown Hills madrasa highlights what can be achieved with training and good community ties. The madrasa is organised along school lines, with classes arranged by academic year. Lessons are fun, says Sheikh Ibrahim Mogra, head of the madrasa. All 20 staff are CRB-checked and receive training, including in child protection. Corporal punishment is prohibited. "Not a single child is scared of me," he says.