School rules: The new row threatening Tony Blair's reforms

The post-war council estates have seen better days, the youth club is shabby and the library derelict. So it's little wonder that parents in Thorne, a former mining town in Yorkshire, were pleased to be told that their local comprehensive was to be replaced by one of the Government's gleaming business-financed academies.

But, as the debate over selection rages within the Labour party, threatening a big revolt over Tony Blair's school reforms, the new Trinity Academy in Thorne, which opened only in September, has found itself at the centre of a row over a strict disciplinary code.

The code is very tough on smoking. Pupils caught smoking are suspended for the first offence, given a final warning for the second and expelled for the third. The same three-strikes-and-out regime exists for verbal assaults on staff.

Parents claim the code, introduced with the new school, is aimed at weeding out difficult children who will damage Trinity's hopes of academic success.

They are not alone in their claims: similar allegations have been made at other academies. Britain's biggest teachers' union, the National Union of Teachers (NUT), says academies are using exclusions to select pupils academically.

The worry among backbench Labour MPs opposed to the Prime Minister's reforms (more than 90 of whom have signed up to alternative proposals) is that the new breed of independently run "trust" school will behave in similar ways to the academies.

At Trinity, the consultation period over whether to establish an academy lasted only two months, hardly enough time to challenge the businessman who was putting up the money, the millionaire car dealer and evangelist Sir Peter Vardy.

But parents were given reassurance from the then Schools minister David Miliband who told them to expect "a successful and popular school [that] will do much to improve opportunities for young people it serves". They all signed up for the project.

Trinity is barely one term old, yet the reality is diverging from the promises. Murmurs of discontent surfaced in the first month, when children were suspended for failing to conform to Trinity's dress code and one couple claimed their son had been turned away at the gates, owing to a suspension imposed by the old comprehensive.

The school is one of 27 new academies up and running - state-funded independent schools that can have their curriculum and ethos shaped by their sponsor so long as he or she invests up to £2m towards building costs.

The Prime Minister is determined to have 200 of the controversial new academies by 2010. They are the prototype for Blair's vision of the future - a network of independently run "trust" schools also given freedom to run their affairs. Critics claim both new types of school will lead to a two-tier system by creaming off the brightest pupils and leaving the rest behind.

Discontent about Trinity's uncompromising disciplinary code reached new proportions earlier this term when more than 200 people packed a protest meeting at a local hotel.

One of the organisers was Janet Barwell, mother of Chris, 15, a pupil who has been excluded permanently after being caught smoking twice and accused of a similar third offence by fellow pupils. Mrs Wood claims that the headteacher, Ian Brew, told her either to move her son to nearby Hatfield Comprehensive or face permanent exclusion. She is worried that may jeopardise his future employment opportunities.

Even the Barwells' Blairite MP Ed Miliband - brother of David, the former Schools minister, appears to be surprised that a Christian academy that his brother promoted wants to expel a pupil permanently for smoking.

"I hope consideration will be given to whether it is proportional to permanently exclude a pupil six months before his GCSEs for an offence which, according to my understanding, was not seen by any teacher," he said in a recent letter to the headteacher. Mrs Barwell last week lost her appeal against the exclusion of her son who has not been at school since 17 November.

The protest meeting also heard about Catherine Hodgeson, 15, who was suspended for wearing the wrong type of trousers that, it transpired, the school's uniform supplier had provided. Another girl had already been suspended six times - on one occasion allegedly for having her hair tied back too loosely.

Most parents believe a dose of discipline does pupils no harm. But the controversy is doing little to dampen suspicions of a deliberate strategy to gradually manoeuvre the more difficult pupils towards comprehensives such as Hatfield, leaving Trinity to improve its academic performance by drawing from its impressive waiting list.

Doncaster council's reintegration officer, Jim Board, who works with the borough's excluded pupils, said as much when he told the public meeting: "We predicted that when the local education authority gave away Thorne Grammar we would see exclusions used in a way we didn't before."

Similar talk has been surfacing at West London Academy in Ealing, sponsored by the millionaire businessman Sir Alex Reed, where 80 pupils were excluded in a year, three times the previous number.

That figure was criticised by Ofsted, the education standards watchdog, which failed the academy. The former head, Alistair Falk, who has since resigned, defended the number of exclusions on the grounds that he was simply obeying the call by Education Secretary Ruth Kelly for "zero tolerance" of bad behaviour.

At the King's and Unity academies in Middlesbrough, 61 pupils were excluded in the two years up to December 2004 - compared with only 15 in all the other secondary schools in the town.

In a document circulated by the NUT to all its branches for use in local campaigns against academies, the union says: "The number of exclusions from academies is far greater than council-maintained schools - so much so that it is obvious that academies use exclusion as an unofficial method of selection."

It adds: "The NUT believes that the money spent on academies is not the best use of funding and has called for an end to the initiative."

Academies defend themselves by saying they are dealing with some of the toughest teenagers in the worst-performing schools and that they have to make a stand on discipline.

At Trinity, the head withdrew from an arranged interview with The Independent that would have included a tour of the school. But his spokeswoman said that - apart from Chris Barwell - only one child had been excluded, for possession of a knife. "We made no secret of the fact that we would have very high expectations of behaviour," she said.

Tracy Morton, a local parent governor, says that she saw all this coming when she successfully campaigned to prevent the Vardy Foundation from building another academy in nearby Conisborough, last year.

"A third of pupils from places like Thorne have special needs, either behavioural or emotional problems," she says. "Some have alcoholic or drug-addicted parents. They need help, not ultimatums. Parents also feel impotent because the school is free from local education authority control and not accountable to its community."

Chris Barwell wants his place back at the school. He has never been suspended before and a certificate he received with a £20 voucher at the end of the last academic year suggests he does have potential, if someone can engage with him and find it. The award came in recognition of "attendance, punctuality, good manners and a positive attitude to his own learning".

Why the PM will have a battle getting his reforms through Parliament

The row over exclusions at Trinity Academy (right) goes to the heart of backbench Labour MPs' fears over Tony Blair's school reforms.

Because his new "trust" schools are independently-run and have control over their own admissions arrangements the fear is that they will introduce a policy of selection by stealth as Trinity has been accused of doing, resulting in a two-tier education system.

Therefore, the Labour-dominated Commons education select committee is calling on ministers to ban interviews with parents and other forms of indirect selection when choosing candidates. Mr Blair may be prepared to swallow these ideas to ensure a smoother ride for his proposals.

However, parents' worries about Trinity show why this concession may not be enough to buy off the rebels because it would not stop selection by exclusion.

In his speech outlining his opposition to the reforms, the former Labour leader Neil Kinnock was scathing of the principles that lay behind the trust schools. They were about creating the new "Chelseas" of the exam league tables, he said.

As a result, some Labour rebels may hold out for something more - such as the disappearance of the trust school idea or stronger powers for local authorities. Charles Clarke, when he was Education Secretary, suggested all schools should be compelled to admit their fair share of problem pupils. Or the rebels might go for another idea backed by the select committee - to set benchmarks for every school showing the percentage of children on free school meals they should be admitting.

Downing Street has already rejected the latter and Mr Clarke came under fire from the grammar school lobby when he suggested the former. It all goes to show that the Prime Minister may still have tough job getting his reforms through even if he does make some concessions. RG