"Disappearing" pupils at academies have led to claims poorer performing teenagers are being "weeded out" to boost grades.
GCSE student numbers dropped sharply at four Croydon academies in the 12 months before sitting the exams last year, provoking a Croydon Council investigation.
Harris Academy South Norwood, where 14 per cent of its 2012 Year 10 pupils had left the school before sitting GCSEs in Year 11, saw the biggest proportion leave.
Oasis Academy Shirley Park saw the largest exodus, with student numbers plummeting from 220 in Year 10 to 196 the next year, according to school census data.
The council confirmed last week it had asked the Department for Education for further information on falling numbers at some of Croydon's academies, although it would not confirm which ones.
The four academies with the biggest drops lost a combined 67 pupils from last year's GCSE cohort, compared to a total of 34 across the rest of the borough's 19 state-funded schools.
Almost all schools saw minor fluctuations in pupil numbers, but the four academies concerned all reported disproportionate drops.
At Quest, enrolled pupils fell 10.9 per cent between Years 10 and 11, while Harris Academy Purley lost 13 students, equivalent to 7.8 per cent of the year group.
Monique Ribeiro, who sits on the management committee for a federation of five pupil referral units that provide places to excluded Croydon students, said academy providers were known to freeze out troublesome youngsters.
She said: "They go in, they want to make it an academy, they need the figures to look good, they weed out the naughty students and all of a sudden they have this very good school with a good reputation".
Although Ms Ribeiro stressed the practice was "not new", academies' increasingly dominance of Croydon's secondary school landscape has caused concern among critics.
Fourteen of Croydon's secondary schools are either academies or in the process of becoming one.
None of the four academies with large drops permanently excluded an usually high number of student last year.
According to figures published by the council, Quest Academy expelled four students across all year groups; Oasis Shirley Park excluded three and Harris Academy South Norwood excluded two.
But Ms Ribeiro said: "It is not just exclusion rates, it is pupils not sitting exams so proportionally their numbers look good.
"Grammar schools have done that for years and so have comprehensive schools, especially some of our Catholic schools.
"Some of them might do managed moves rather than exclusion, because you need to have a good excuse to exclude a pupil now."
David Clark, headteacher at Archbishop Lanfranc School, agreed it would be "a false premise" to assume exclusions were the only way of removing students from a school's roll and urged the council to establish how and why students were vanishing from some academies.
He said: "I am pleased the matter of 'the disappearing pupils' seems to be being explored more thoroughly than has been the case when the issue has reared its head previously.
"If pupils are being removed from school rolls for less than good reasons, it raises more serious questions about a climate and system which encourage people to the view that it is OK to do so."
David Clark, headteacher at Archbishop Lanfranc School
He added: "I am sure the interest in the possibly disappearing children has been prompted by the performance tables and what is being interpreted as an attempt to manipulate the data regarding results.
"What needs to be understood however is that, if children are being removed from school rolls without following due process, this represents a major safeguarding issue which is potentially more significant than league table positions."
All three academy providers said fluctuations in their pupil numbers occurred naturally.
A spokeswoman for Harris Federation, which runs six schools in Croydon, said: "Everyone knows and accepts that London is a particularly turbulent part of the country and that many of its schools have to deal with this on a year-by-year basis.
"When families move away from an area we always do our best to make sure their child can remain in school, but this is not always possible."
An Oasis spokesman said many of its pupils had "a higher degree of transience than average," adding: "This, in turn, can and does cause fluctuations in numbers as a cohort progresses through an academy."
Oasis's second Croydon academy, in Coulsdon, saw a slight increase in Year 11 pupil numbers last year.
A Quest Academy spokeswoman suggested the drop last year had been a one-off "historical hangover" from the school's conversion from Selsdon High.
A spokesman for the DfE said: "Under no circumstances should a school remove a pupil from its roll on the basis of their academic potential or results.
"All schools must follow clear regulations when removing a pupil from their roll."
Have you or has your child been forced to leave a school or academy in Croydon? Call the newsdesk on 0208 722 6351 or email email@example.com.
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