The Mosque and Imams National Advisory Board (MINAB) recognises the problem of abuse in the after school classes.
Ahmed Beg, from the board, said: "We are working to raise standards and want the teachers to be qualified."
Irfan Patel, 33, was found guilty on Friday of cruelty against children at a Lancashire mosque.
A Lancashire mother, who wanted to remain anonymous, was horrified to discover her son's madrassa teacher had been hitting and abusing him.
"I never sent him to be beaten - I sent him to learn the Koran," she said.
He was not the only one to suffer at the hands of a teacher at a madrassa, an after school class where children learn about their faith.
In the last year, three teachers from madrassas in Lancashire have been convicted of beating children, the latest case involving Patel.
In August Kurram Hussain, also from Blackburn, was found guilty of what magistrates called "gratuitous degradation" in beating two boys aged 10 and 11.
That followed Ibrahim Yusuf's conviction while teaching at an Accrington madrassa in 2011.
The mother said police had told her that her son's teacher had punched him in the stomach and "slapped his face, and hit his hands with a pencil".
"And he made him stand like a chicken. If he fell down, after five minutes my boy said he made him do another five minutes."
The stress position her son was forced to adopt is a torture tactic used in war zones.
Corporal punishment has been banned in mainstream schools since the 1980s.
However, madrassas are classed as supplementary schools where it is still legal in religious settings as long as it does not exceed "reasonable chastisement".
The schools are unregulated and teachers often have no training.
Nazir Afzal, the chief crown prosecutor for north-west England, handled all three prosecutions. He thinks abuse is far more widespread.
"When we talk about three successful prosecutions in the last year in the North West and probably a dozen nationally, we're talking about literally the tip of the iceberg," he said.
"In order to meet the demand, schools are being set up left right and centre.
"There is no Ofsted, no inspection regime, they're reliant entirely on a particular committee enforcing standards, ensuring discipline is correctly maintained.
"And if they are not up to the job, there's nothing to prevent children being harmed pretty much on a daily basis."
One school leading the way in the reform is Jamia Ghosia Academy in Blackburn.
It has become more like mainstream schools and is seen as a model of good practice by teachers at madrasssas in other parts of the country.
Classes are small and interactive, staff are checked for criminal records, CCTV is in place to protect pupils and corporal punishment is banned.
Head teacher Ustad Muhammad said: "In terms of corporal punishment, I'm not going to accept that in any form or any way because no child learns with that.
"You have to be patient. Children can be rowdy, can shout, can do certain things but that's the whole idea of having teacher training and learning certain types of skills."
An Islamic watchdog is calling for the reform of madrassas following the latest conviction of a teacher for child cruelty.