Almost 10,000 pupils are so unruly they are being kept out of school and sent on special behaviour improvement courses, the Government has claimed.
Headteachers unable or unwilling to exclude children are using other ways to ban them from the classroom, including making them have anger management training, according to the Department for Children, Schools and Families.
But officials claim schools are abusing their powers by using vague laws as a way of keeping pupils from lessons without their parents' knowledge.
New regulations, due to come into force this September, will make it more time-consuming and bureaucratic to allow pupils to miss normal school.
The DCSF says more than 9,000 children are being educated "off site" every year. This is legal, but officials say it leaves children vulnerable, especially those with special educational needs.
Heads must now give advance written notice to parents and hold regular meetings about the pupil.
The behaviour and anger management courses are either run by schools themselves or at pupil referral units, and the time spent on them varies according to the pupil.
A new consultation document says: "There is a risk that this power is used by schools to keep difficult pupils off mainstream school. Therefore, government intervention is necessary to prevent indefinite referrals. This will ensure equitable treatment for all pupils.
"The objective of the regulations and guidance is to ensure that the power is used appropriately as a tool to improve behaviour and not just a way of removing pupils from the school," it adds.
Behaviour expert Fintan O'Regan argued that inclusion had led to a situation where teachers can't cope with difficult pupils. "It is clear they are trying to be innovative. But if the Government is going to create these loopholes, it should be surprised if they are occasionally used in sinister ways," he said.
The Government's behaviour "tsar", Sir Alan Steer, condemned unofficial exclusions during the years he spent preparing new guidance for teachers. He supports the new rules.
"Nobody wants to stop schools being creative, especially if they are keeping children away from school so they can get a personalised curriculum, but this needs to be done properly," he told The TES.
At Northampton School for Boys, pupils have been referred for anger management classes. But headteacher Mike Griffiths doesn't believe in sending children away.
"It's very important to be clear about what's happening to them, we like to track changes ourselves and they need to be in school," he said.
"Doing this all unofficially masks problems. It just creates a trail of disappointment. If it's official there tends to be more effort put in to sorting out bad behaviour and this stops the merry-go-round situation."
Darren Northcott, assistant secretary of teaching union the NASUWT, said teachers should notify him of cases where children have been treated unfairly.
"We would hope they would all use their professional judgment about what's best for the child and the community," he said.
"But I would say having a meeting about the child every 30 days is out of proportion, it should be decided on a case-by-case basis."
WHAT IT MEANS
- The Education and Skills Act 2008 allowed teachers to send children away from school. The Department for Children, Schools and Families (DCSF) says this can lead to poor schooling. Parents have no right of appeal.
- Anger or behaviour management courses are also used when schools are reluctant to go through the legal exclusion process, possibly because the decision could be overturned.
- The impact of the DCSF's new rules could be expensive. Behaviour meetings will have to be held once a term and the cost of this is estimated to be #163;27 million.
- The current legislation was set up to allow "managed moves" - when children are transferred to another school. Concerns about its impact on children were raised during its progress through Parliament.