David Cameron overruled strongly worded civil service advice so that his special advisers would get an extra £282,000 in severance pay because of his resignation.
Civil service chief executive John Manzoni insisted the Prime Minister would have to order him to boost golden goodbye packages for long serving special advisers from the 4.5 months pay stated in their contracts to the six months worth of wages Mr Cameron wanted them to have because he "strongly" disagreed with the move.
Mr Cameron's decision would send the severance pay bill soaring by £282,892, taking it from £747,045 to £1,029,938, and set a precedent across all Government departments which could lead to another 30 special advisers getting the same deal, the top civil servant warned.
Mr Manzoni wrote "I do not believe there is a case for awarding higher sums than those for which the contract allows. Legal advice supports this position, and lawyers have been clear that awarding a further month's salary for special advisers in this position would constitute a payment above the contractual entitlement.
"My strong advice is that we continue to abide by the provisions in their contracts of employment.
"The contract itself is designed to provide some degree of certainty and security for individuals who take on these roles in the knowledge their appointments may come to an end at short notice."
Mr Manzoni, who is also Cabinet Office permanent secretary, wrote: "If the Prime Minister's view is that we should nevertheless proceed with awarding six months' severance pay I will proceed accordingly, but I would request his written direction in order to do so."
The top civil servant said that if a written direction was issued he would have to inform the financial watchdog, the Comptroller and Auditor General, of the matter, who in turn was likely to inform the Common's powerful Public Accounts Committee which could probe the affair.
Mr Cameron's principal private secretary, Simon Case, replied to Mr Manzoni that the then PM would issue the direction regarding the long serving special advisers who were reappointed after last year's election, because: "He is conscious that the situation they find themselves in is through no fault of their own.
"The termination of their employment has been sudden and unexpected, and he does not wish to exacerbate an already difficult and uncertain time for them by inferring that their long and loyal service is not fully recognised."
Mr Case, who said Mr Cameron wanted the six months rule applied across Government, sent the letter on Wednesday - the day Mr Cameron quit Downing Street for good - in response to Mr Manzoni raising his concerns the previous day.