A TES investigation reveals that 13 of the schools turned into academies had total debts of nearly pound;5.9m.
Worst offender was Ducie high school in Manchester, which had a deficit of pound;1.86m before it became Manchester academy in 2003.
Evelyns community school, in Hillingdon, west London, had run up a Pounds 739,000 deficit before becoming Stockley academy two years ago. In the same borough, John Penrose had a pound;150,000 deficit before it became Harefield academy this autumn.
This year, Malory school, which was pound;450,000 in the red, became Haberdashers' Aske's Knights Academy, in Lewisham, south London.
Two councils said central government grants covered some or all the losses, but in the case of Ducie this still left a pound;400,000 absolute loss.
Ed Davey, Lib Dem education spokesman, said: "Head teachers and governing bodies are being bribed to become academies and not necessarily acting in the wider interests of education.
"This creates tensions with the family of schools when we need ...
Martin Rogers, of The Education Network (Ten), which is supported by local authorities said: "If other schools are expected to pick up the tabs, they might not be that popular with other heads."
Sarah Caton, the assistant director of the Confederation of Education Managers, said: "You have to wonder whether this position - that LEAs pick up the tab - is sustainable in the long term."
A government spokesman confirmed that LEAs are responsible for the deficits of schools that become academies.