The "battle" raging between Tony Blair and Gordon Brown is harming the way the machinery of government is working, BBC News has been told.
Mr Baume's comments will reignite claims of a rift
Jonathan Baume, who represents the UK's top civil servants, said the situation had worsened in recent months.
What the chancellor wants implemented is "not by any means what Alan Milburn and the prime minister want to see".
Number 10 said ministers were interested in governing and not a "soap opera" about Mr Blair and Mr Brown.
First Division Association's leader Mr Baume made his claim on the day Mr Brown was due to deliver his pre-Budget report.
In an interview with BBC Radio 5 Live, he said there were sometimes "conflicting and competing agendas for government" between Number 10 and the Treasury.
"Government departments get their money from the Treasury on the basis of public service agreements they sign up to, but at the same time the prime minister also has an agenda and that's not necessarily the same as the Treasury's and the prime minister is of course a very powerful figure in any government," he said.
"He also sends instructions and messages and directions to departments about how he would like each secretary of state and each department to implement a policy agenda.
"The problem is that on many occasions these two don't add up and individual cabinet ministers as well as departments have to make sense of this battle."
Mr Brown is due to set out his stall for the next election on Thursday delivering his assessment of the British economy and predicting measures in the coming Budget.
The pre-Budget report follows the Queen's Speech which stressed measures to tackle crime and the terrorist threat.
It also coincides with the publication of government plans to overhaul childcare.
Mr Brown's former adviser Ed Balls, who is hoping to win a seat in Parliament, dismissed Mr Baume's claims as "silly fourth hand gossip".
He said: "The fact is that today Tony Blair and Gordon Brown together are setting out long term plans on skills, on childcare on science and together as well which is what governments do."
Tory shadow chancellor Oliver Letwin said: "The battle Royal that the top civil servants are now reporting on between the chancellor and Tony Blair is
preventing them both from getting on with the business of getting taxpayers value for money."
Mr Baume's comments come ahead of a new book by journalist Robert Peston which will reportedly say the chancellor is setting out his own policy platform because he believes Mr Blair will not hand over power to him voluntarily.