Whitehall mandarins are wary of raising the alarm about failing government projects because they do not want to damage their careers, according to a report.
The National Audit Office (NAO) warned that implementing the wishes of ministers appeared to be receiving more emphasis than "value for money".
Senior officials in departments can signal their concerns about a policy by asking for a formal "ministerial direction" to press ahead.
But the watchdog found the mechanism was "not being used effectively as an accountability control to safeguard value for money".
"Where an accounting officer has serious concerns about value for money, he or she can flag the concern to Parliament by formally (and publicly) requesting a direction to proceed from the minister," the report said.
"The threat of this can prevent poor decisions about use of taxpayers' money, but evidence suggests the mechanism is not being used effectively.
"Many major projects where there were clear value for money concerns, such as implementation of the Single Payment Scheme for farmers (2005-2014) or the National Programme for IT in the NHS (2002-2011), have not been the subject of directions."
The auditors said it was possible the threat of requesting a direction was being used "invisibly" by officials, but there was no evidence of how widely that was happening.
"Accounting officers appear to lack confidence to challenge ministers where they have concerns about the feasibility or value for money of new policies or decisions, not least because standing up to ministers is seen as damaging to a civil servant's career prospects," the report said.
The NAO said the situation was not a "recent phenomenon", but had been developing over time as ministers took a more "executive" role over policy and sought "greater involvement" in the selection of civil servants.
NAO head Amyas Morse said accounting officers had always needed to balance their responsibility for obtaining "value for money" against duties to execute policy and support ministers.
"I think that these ministerial and policy goals have come to weigh more and more heavily," he said.
"The ever-increasing influence of special advisers, and ministers' greater involvement in policy implementation and Civil Service appointments, is pressing down on the 'ministerial' end of the see-saw further and further, while considerations of value for money and public value rise steadily into the air."
A Government spokesman said: "The Government is committed to delivering value for every pound of taxpayer's money that we spend, and doing more with less. Over the last Parliament we made real progress - spending on public administration fell by 40% while public satisfaction with local services increased, and crime was down by a quarter.
"The recent Spending Review set out the next stage in our plan, to continue doing more with less while getting Britain back into surplus by 2019/20.
"The Government has also introduced far-reaching reforms to increase accountability and transparency over our spending plans, including publishing the 'Whole of Government Accounts' annually and ensuring that senior civil servants in charge of major public projects can be called before Parliament.
"It is disappointing that the NAO have chosen not to reflect the full facts in their report which has been published today."
Julian McCrae, deputy director of the Institute for Government thinktank, said: "Today's NAO report is a reminder of the important issue of accountability, which has dogged successive administrations. While this Government has overseen some positive developments, such as making senior civil servants more clearly accountable to Parliament on major projects, more needs to be done.
"Ministers, special advisers and permanent secretaries must work together to understand each other's roles and work together more effectively.
"The question of who is responsible for what in government has been fudged so many times, and in so many high-profile cases, that trust in the system has all but broken down. When things go right or wrong, it must be made clearer who is responsible and what are the consequences for that failure or success."