Pupils at academies are twice as likely to face repeated temporary exclusions or be permanently expelled than those in mainstream secondaries, Government statistics show.
In mainstream secondaries, 3.8 per cent of the school population was given more than one suspension in the 200809 academic year, while in academies this was 7.27 per cent.
A total of 13.5 per cent of all pupils in academies were suspended at least once, compared with 9.26 per cent in secondaries.
These figures do not take into account that most existing academies operate in areas with above average deprivation. Indeed, the figures show that poorer children are much more likely to receive the punishment: 22 per cent of secondary pupils eligible for free school meals were suspended during the 200809 academic year, compared with 7.38 per cent of pupils who do not claim the benefit.
Fixed-period exclusions are usually given when children do not co-operate with teachers, and for minor offences such as bringing mobile phones into lessons.
Some experts say greater freedom and less scrutiny "encourages" academy heads to use the punishment.
Andy Winton, past president of the National Association of Social Workers in Education, said the fact academies had freedom from local authority control made heads and teachers more likely to exclude.
"They have greater autonomy and are subject to less scrutiny, so they can do what they think inspectors will want without having to also do what council officers want," he said.
"The problem is the more often you exclude children, the more they become disenfranchised and end up being an underclass."
Pupils at academies were twice as likely to be permanently expelled. The statistics show 0.31 per cent of academy pupils were permanently excluded, compared with 0.17 per cent of pupils in secondary schools.
Children eligible for free school meals were also twice as likely to be permanently excluded than all pupils. And for children with special educational needs but without a statement, the proportion receiving exclusions was three times the proportion of all pupils.
John Bangs, head of education at the NUT, said academy heads felt they had Government "approval" to exclude more often.
"The previous Government disapproved of exclusion, but this attitude never extended to academies because they wanted them to succeed. There was almost an encouragement that this was the right thing to do in order to get results," he said.
"The current Government seems more supportive of exclusions and with more academies on the way we could see a rise in the number of exclusions and therefore more children confined to the scrapheap."
The education parliamentary select committee's inquiry into behaviour and discipline in schools will examine the use of fixed-term and permanent exclusions.
A Department for Education spokesman said: "Academies often inherit a large number of disengaged pupils and need to establish good behaviour in order to raise attainment. Academies place great emphasis on getting the basics right and improving behaviour, in particular.
"The 'outstanding' schools that choose to convert to academy status from September 2010 will be operating in very different circumstances from most of the earlier academies that were established to replace schools in challenging circumstances.
"It is unlikely that we would see any significant changes in exclusion figures in relation to these 'outstanding' schools."
Comment, page 25.