The Cabinet Office minister has accused the civil service of drafting a job description for permanent secretaries without "constitutional propriety".
The document sets out the qualities for permanent secretaries, who are the UK's most powerful government officials.
Francis Maude criticised a suggestion they had to balance ministers' needs with their departments' long-term aims.
The Cabinet Office said the document did not reflect the constitutional position and was being updated.
The incendiary accusation by Mr Maude follows his discovery of the official civil service document, which has been passed to BBC Newsnight and the Times by a source outside of government.
It says that a permanent secretary must "balance ministers' or high-level stakeholders' immediate needs or priorities with the long-term aims of their department, being shrewd about what needs to be sacrificed, at what costs and what the implications might be".
In a letter to cabinet colleagues seen by Newsnight, Conservative Mr Maude says: "As currently framed [the document] plainly does not conform with constitutional propriety.
"The civil service aims not to serve the 'long-term aims of the department' but the priorities of the government of the day."
'Serve the government'
The civil service code of conduct, the main official document setting out guidelines for all of Whitehall, says only that civil servants "serve the government, whatever its political persuasion, to the best of your ability in a way which maintains political impartiality".
But this previously unseen document, written in 2009, was intended to set out the criteria by which permanent secretaries would be chosen.
It is still in use and in recent weeks civil servants brought it to the attention of Mr Maude, suggesting he update it.
Using descriptions that have enraged cabinet ministers, it says civil servants must "tolerate ambiguity" and deal with "at times irrational political demands".
'Beyond a joke'
The document continues: "[Permanent secretaries] act as a 'pivot point' in terms of knowing when to 'serve' the political agenda and manage ministers' expectations, versus leading their department with a strong sense of mission."
Former Conservative minister Nick Herbert told Newsnight: "I think this is an extraordinary document. This is actually beyond a joke.
"We can't have a kind of permanent government of an unelected bureaucracy deciding that it has its own long-term priorities which may be different to those of ministers and elected government.
"And I think this does go to some of the problems that we're seeing of a civil service which is sometimes resistance to change."
Former head of the civil service, Lord Butler, said the document seemed to be an accurate summary of the relationship between civil servants and politicians.
"Ministers have a political agenda which civil servants can't get into," he said.
"Although you're working very closely together, you've got to keep a bit of difference between yourselves."
He added: "There is nothing there that I wouldn't have put down in black and white... some of it could have been a bit more straightforwardly expressed but... I think it does reflect the borders that permanent secretaries can't cross."
Mr Maude's comments are the latest salvo in an increasingly bitter fight over Whitehall reform.
Elsewhere in his letter to cabinet colleagues, Mr Maude gives the prime minister an audit of the programme of civil service reform.
He writes: "Productivity has markedly improved since 2010, with a civil service 17% smaller delivering at least as much as before.
"However, it remains far from clear how much real and lasting reform can be achieved.
"The first civil service commissioner himself, David Normington, recently questioned 'whether the reform agenda matches the scale of the changes needed'."
He adds that the "greatest challenge" is probably to change the civil service's culture, saying "younger, high potential civil servants" had been asked to draw up plans to address this.
A Cabinet Office spokesman said of the document: "The constitutional position is clear that the civil service exists to serve the government of the day, while retaining the potential to serve a future government.
"A document laying out the criteria for permanent secretary candidates from 2009, which predates both this government and the leadership of the civil service, did not reflect that position and is therefore being refreshed.
"Permanent Secretary appointments are made on merit following fair and open competition."