The commission puts receivers and managers in interim control of a charity when there are serious concerns about how the organisation is being run.
In the biggest case of 2004/5, the commission safeguarded £19.5m belonging to Christian charity the King's Ministries by installing personnel from KPMG at a cost to the charity of £200,000.
John Weth, chairman of the Association for Charities, said: "We have expressed concerns about aspects of receiver and manager appointments.
We trust that with the tightening of lines of accountability within the commission, and the close attention being paid to the monitoring of interim managers, we shall see far fewer - if any - causes for concern."
Andrew Hind, Charity Commission chief executive, said: "We want to be wholly transparent about the facts surrounding receiver and manager cases."