Croydon Council has asked the Department for Education to investigate why pupils have been "disappearing" at two academy chains' schools ahead of sitting GCSEs.
The council has requested additional data from the department on falling pupil numbers Harris Federation and Oasis Community Learning, which together run nine academies - six of them secondary - in the borough.
It follows an investigation by the Guardian that found 7,500 pupils vanished from GCSE year groups across the country during 2012-13.
Harris and Oasis, two of England's largest chains, had several schools with large drops.
Harris Academy South Norwood, in Cumberlow Avenue, had 22 per cent fewer pupils sitting the exams than were in the same year group three years earlier as 12- and 13-year-olds.
The year's numbers shrank particularly sharply in the run-up to the GCSEs, falling from 197 to 169 between January 2012 and 2013.
Out of the 50 schools which saw the biggest gap between their GCSE pupils last year and the same year group in 2010, Harris had six academies and Oasis three.
It has led to suggestions schools may be benefiting from pupils with poorer academic potential leaving, although there is no evidence to such they are doing so deliberately.
Both providers said pupils were never exclused on the basis of academic performance.
A spokeswoman for the Harris Federation 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 the communities we work in are subject to a number of circumstances that cause them to have a higher degree of transience than average.
"This, in turn, can and does cause fluctuations in numbers as a cohort progresses through an academy."
Croydon Council confirmed it had requested additional data from the Education Funding Agency, the branch of the DfE that monitors some aspects of academies' performance.
The council would not confirm which academies, but it is understood the information requested includes pupils' reasons for leaving schools run by Harris and Oasis.
A spokesman said: "On the basis of the partial information we have we’ve written to the Education Funding Authority. We now have to see what action they take."
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."
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