Whitehall's most senior civil servants formally protested over a spending spree by Labour ministers during Gordon Brown's final months in power.
Departmental permanent secretaries took the "nuclear option" of asking outgoing ministers to put their decisions in writing by signing "letters of direction" officially authorising the expenditure.
The letters made it clear that the decisions – believed to have involved defence contracts, consultancies and procurement – were made not by civil servants, but by their political masters.
The unusual move was disclosed by the First Division Association union (FDA), which represents senior civil servants.
Jonathan Baume, its general secretary, told the BBC: "When a permanent secretary asks for a letter of direction from the minister, it is because they feel that a serious decision is being taken which they feel is not right."
Permanent secretaries require them because their position as the department's accounting officer makes them responsible for vouching for the propriety, regularity and value for money of its activities.
Asked how many letters were issued, Mr Baume replied "a number". Precise details were likely to be made public by the House of Commons Public Accounts Committee when it reconvenes, he said.
He added: "The fact that a permanent secretary feels the need to ask for a letter of direction indicates... a serious disagreement about that particular decision."
His disclosure supports ministers' claims that the Labour administration was reckless with public money ahead of the election, leaving "black holes" in their budgets.
David Laws, the new Chief Secretary to the Treasury, has ordered a reappraisal of all major spending decisions taken since 1 January. He said the Government had discovered spending decisions were made by Labour ministers "against accounting officers' advice".