Fees for running the Futurebuilders programme from 2004 to 2011 will be £29m, or 16 per cent of its total value, according to figures released last week.
Ministers have consistently described Futurebuilders, used for loans and grants to help voluntary organisations win public service contracts, as a £215m fund.
After the fund closed for applications last month, the Office of the Third Sector admitted that £31.3m had been returned to the Treasury unspent, leaving the total at £183.7m (9 February, page 3).
Last week the OTS confirmed that fees paid to the two organisations that have administered the fund had cut the amount available to £154.7m.
"The Government has short-changed the sector," said shadow charities minister Nick Hurd, a former fund manager. "£31.3m has been lost and a further £29m swallowed up in ridiculously high management fees.
"They promised a £215m fund but only £154.7m will be invested - and that is assuming all loans are drawn down. Shabby, even by their standards."
Jenny Willott, charities spokeswoman for the Liberal Democrats, said: "Any underspend or reallocation of funds designed to help charities win government contracts is a travesty."
A Cabinet Office spokesman said it was normal to include administrative costs in investment figures. He said the complex, experimental nature of Futurebuilders justified the fees.
"The Government took a calculated risk to invest in this programme and, though there are many sceptics, with the hard work of the delivery partners we have managed to make it work," he said.
Jonathan Lewis, chief executive of Social Investment Business, which has managed the fund since 2008, said any profits from the £12.3m it was being paid in management fees were being divided between SIB, which is a social enterprise, and its parent charity, the Adventure Capital Fund. "Not a single penny has been distributed to individuals," he said.
SIB could receive an additional £230,000 for hitting its targets, said Lewis. The organisation provided value for money, he added: "We have spent an awful lot of money driving up demand for loan finance and we provided several million pounds of business support."