At least a quarter of all free schools have overestimated their pupil rolls, resulting in payments of more than £40 million for unfilled places.
And the government has written off another £1.3 million for schools that have struggled to recruit pupils or have closed, a Freedom of Information response from the Department for Education reveals.
The most recent write-off was for the troubled Collective Spirit free school in Oldham, which closed at very short notice last summer after it had been placed in special measures the year before.
It had £248,661 written off in 2016-17 – the latest year for which figures are available.
Money clawed back from free schools
The FoI response shows that 332 free schools that opened in the four years to 2016-17 have been funded based on the number of pupils they expected to recruit.
During that time, £41.4 million has had to be clawed back from schools that failed to attract as many pupils as planned. However, only £31.5 million has so far been recovered.
In 2016-17 alone, 138 free schools had to pay back a combined £11.9 million as a result of these "pupil number adjustments" (PNAs). That represents 29 per cent of the 473 free schools open as of September 2017.
But the actual proportion is likely to be significantly higher because the 138 does not include university technical colleges. It also only covers a single year, as the FoI response did not allow the calculation of a reliable combined figure for all four years.
Usually, the money for empty places is recouped from free schools automatically via the main government grant they receive.
But the FOI shows that £10 million is owed by free schools that have been given longer to pay back the money because they have signed, or are in the process of agreeing, "recovery plans" with the DfE.
'Far more efficient ways' to open schools
National Education Union joint general secretary Mary Bousted said: "These figures show that parents aren't attracted or sending their children to free schools in sufficient numbers that fulfil the schools' contract with the DfE.
"And that raises clear questions about the need for these schools in their [areas] and whether there aren't far more efficient and effective ways for schools to meet the needs of the population."
She highlighted the findings of the National Audit Office, showing that 57,500 out of 113,500 new places in mainstream free schools opening between 2015 and 2021 would create "spare capacity" in the immediate area.
A Department for Education spokesperson said: "Funding that is provided to set up new free schools and university technical colleges is based estimates on pupil numbers. Once the school or UTC opens, this funding is then adjusted to reflect actual figures and where necessary, we work with the institutions to recover funding.
"We have agreed recovery plans in place for most free schools and university technical colleges that have pupil number adjustments, and we are in discussion with the others about terms for recovery.”
A spokesperson for the New Schools Network said: "The DfE is very clear about prioritising free schools in areas where there simply aren't enough places - 83 per cent of new free schools have opened in precisely these areas.
"What's more, free schools are more likely to be oversubscribed than any other type of school - they continue to be hugely popular with parents across the country."