The proportion of students in schools for excluded pupils in inner London is almost double the national rate, according to new analysis which raises concerns over the increasing exclusion rates from schools in England.

Research found that one in 116 pupils in the 13 inner city boroughs of the capital are in schools for excluded students – rising to one in 54 in one London borough, compared with the national figure of one in 196 pupils.

The rate was calculated by looking at headcount of students in pupil referral units as a proportion of all secondary school pupils.

This latest research was carried out by a new education charity called The Difference, set up to train a new generation of specialist teachers to help stem the flow of excluded pupils out of mainstream schools, first in London and then across England.

Kiran Gill, charity founder and fellow of the Institute for Public Policy Research, said: “I think we need to ask seriously whether the London story of school improvement has left some of the most vulnerable behind.”

London’s schools are among the highest performing in the country, having undergone a radical transformation as a result of the London Challenge programme which saw huge improvements in the capital’s schools between 2003 and 2011.

However experts in the sector are concerned about the proportion of pupils who end up leaving high-achieving mainstream schools in inner London and moving into pupil referral units (PRUs) or other alternative provision (AP) for excluded students.

School exclusion rates in England are coming under increasing scrutiny from government and the schools watchdog Ofsted. Last year saw the third successive annual increase, which ministers acknowledge is a concern, though they point out the numbers are still far fewer than the peak 10 years ago.

According to official government data, Blackpool has the highest proportion of students in schools for excluded children with one in every 30 secondary school pupils in a PRU – or 3.3% – which is six and half times the national average.

But many of the inner London boroughs are among those with the highest proportions in England – in Kensington & Chelsea it is one in 54 pupils in a PRU (1.8%), in Islington, it is one in 65 (1.5%), in Camden one in 76 (1.3%) and in Haringey one in 84 (1.2%). The national average proportion of children in PRUs is 0.51%.

Education secretary Damian Hinds is due to appear before the education select committee next week when he is expected to be quizzed about rising exclusion rates, ahead of the publication of the government’s review into school exclusion, chaired by Edward Timpson, which is expected in the next few weeks.

According to Gill, the most vulnerable children with the most complex needs are disproportionately affected by exclusion, and London has large numbers of them.

“Exclusion is correlated with multiple and overlapping layers of disadvantage,” she said. “Growing up in a low-income household, but also having other strains on a child outside of the school gates, like criminal exploitation, grooming and gangs. We know that’s a particular problem in London at the moment.”

With mounting concern about the increase in knife crime in the capital, there have been reports that some gangs are giving knives to pupils in order to get them excluded, thereby making those children more vulnerable to gang pressures.

“In London we’ve got some really exceptional PRUs where mainstream teachers know that if they do refer there, then their students will receive a good quality education,” said Gill. However, the overall picture is bleak. Nationally pupils in PRUs underachieve on a spectacular scale – while 59.1% of pupils will manage a 9-4 pass in English and maths GCSEs, in PRUs and AP it’s just 4.3%.

“I don’t think it’s fair to say that London has some of the least inclusive schools, but I do think in some local authorities where PRU and AP populations are high but quality is low, we need to seriously prioritise both improving AP quality and reducing school exclusion.”

Gill’s new charity will launch a Teach First-style fast-track career programme on Saturday, inviting applications from top quality teachers to train for leadership roles in the sector serving excluded pupils. Successful candidates will spend two years in some of the capital’s best schools for excluded pupils, returning to mainstream with new skills to support vulnerable pupils and reduce exclusions.

Sir Tim Brighouse, architect of the London Challenge, will be among those speaking at the launch. “The greatest challenge facing schools is the pandemic in mental ill health among young people,” he said.

“The Difference leaders’ programme will create a new generation of school leaders with skills to support the city’s most vulnerable learners, and to reduce school exclusion.”

The Department for Education said since 2010 it had taken decisive action to empower teachers to tackle poor behaviour in schools. “Permanently excluding a child from school should only ever be a last resort, but it is wrong to assume that all children in pupil referral units and alternative provision have been excluded from other schools,” a spokesman said.

“The department firmly believes that all children, regardless of the setting, should receive a good education and that is why we have committed to reforming alternative provision. We have already made progress and have launched a £4m AP innovation fund which is delivering projects to improve outcomes for children in alternative provision.”

‘Here, they are the ones who adapt to your needs’

Dré Clinton-Barnes, 15, was just 23 minutes into his introductory day at Mossbourne Community Academy in Hackney when he fell out with a teacher and was asked to leave. It was an inauspicious start.

He and his mother met with staff the following day and Dré returned to classes, but his school career at the celebrated London academy was beset by detentions and isolations. “I talk a lot. I like to have the last word all the time.”

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His home life was complex, with periods in foster care. He kept running away and ended up being placed in a care home in Ashford in Kent where he cried himself to sleep every night for two weeks. “After that it was calm.”

Dré was home-schooled, then got a place at a local secondary school which lost patience with him when he got into a fight. After he was robbed at knife-point, his mother brought him back to London where he struggled to find a school that would accept him.

He is now a student at Wac Arts college in Camden, north London – an alternative provision free school for 14- to 19-year-olds, specialising in creative arts and media – and is thriving.

“The schools I’ve been to don’t really have patience,” said Dré. “They have a thousand other kids to deal with.” He doesn’t blame them. “I was distracting the class,” he said. In any case things have ended up well.

“I live by a philosophy – everything happens for a reason. Here it’s nice. They have more time for students because there’s less students here and teachers explain the work more.”

Giulianna Barbosa, 15, has had a similarly disrupted education. She comes from a complex background and has dyslexia. She went to four different primary schools and her time in mainstream secondary school was spent mainly in isolation.

“My family says that trouble finds me. I come out of class and there’s a fight. I’m the one that gets isolation for it and I’ve got nothing to do with it,” she said. “I had big arguments with teachers. I kept on being accused of stuff that was nothing to do with me.”

Like Dré, Giulianna was never permanently excluded but was the subject of a managed move to Wac Arts college, which suits her interest in creative arts and provides a more flexible approach than mainstream.

“They don’t have patience,” she says of mainstream schools. “They never understand. They are very straight. They will not bend for anything. Here [at Wac], they are the ones that adapt to your needs, rather than you adapt to them.”

College principal James Fornara says the rise in exclusions is directly linked to the way schools are now measured through school league tables, which means teachers are under pressure to focus on tests and getting pupils through qualifications. “Young people like Dré and Giulianna who have complicated and challenging lives can’t fit into those boxes.”