The Public Accounts Committee found a "lack of clarity" over the role of the Treasury, Downing Street and the Cabinet Office in reforming services.
Meanwhile, ministers had to overcome "resistance" among some civil servants to change, it added.
But the government said it had strengthened efficiency in Whitehall.
The committee found disagreement within government, saying: "The civil service remains committed to departmental autonomy whilst ministers want an effective, smart and challenging centre.
"This lack of agreement means that there is no clear definition of the role of the centre and the accountabilities for implementing cross-government initiatives are not always clear."
The committee cited problems with Work and Pensions Secretary Iain Duncan Smith's Universal Credit benefit reforms, which had to be "reset" last year amid concerns over progress.
It also said there had not been an "overall strategic view of risks" in relation to NHS reforms.
The committee's chairwoman, Labour MP Margaret Hodge, said: "Confusion exists at the heart of government about what exactly the role of 'the centre' - Number 10, the Cabinet Office and HM Treasury - should be.
"This current lack of clarity about the precise role and responsibilities of the centre jeopardises government's ability to deliver value for taxpayers' money in key public spending areas."
Mrs Hodge said the centre of government "often responds only after crises occur rather than picking up on the warning signs".
Departments were making "unacceptably slow progress" on some efficiency initiatives, such as shared back-office services and debt collection, she added.
But a government spokesman said: "As part of this government's long-term economic plan, we have worked since the 2010 general election to strengthen commercial, project management and digital capability at the centre of Whitehall.
"Last year alone, the Efficiency and Reform Group worked with the Treasury and departments to save taxpayers Â£14.3bn compared with a 2009-10 baseline. There's more to do to improve efficiency but we have just appointed a new chief executive to accelerate reform and strengthen control over key functions.
"We thank the committee for their report and will consider the recommendations carefully."
Taxpayers are getting poorer value for money from government projects because of "confusion" over decision-making, MPs have warned.