Principal Martin Jenkins and his deputy Jenny Dolphin, were stood down after a meeting between the college's board and FEFC officials last Friday.
The FEFC called for them to be suspended when it began investigating the college three weeks ago but the board initially refused to do so.
The move follows the initial report of independent auditors Robson Rhodes into allegations of misuse of public funds at the college, details of which were exclusively revealed in The TES two weeks ago.
An FEFC statement said that no evidence had been found to support allegations linking particular governors to the procurement of computers or to the college use of hotels.
However, in a letter to college staff, clerk to the governors Peter Hattam, admitted that there were some issues concerning college activities which give the FEFC "cause for serious concern".
He added the principal and vice principal had not been suspended as part of disciplinary procedures.
Christine Tyler, head of the faculty of business, humanities, science and technology, has been appointed acting principal. Investigations by theFEFC and the auditors are expected to last six weeks.