The new GP contract in England has cost the government £1.76bn more than predicted in its first three years but productivity has fallen, says a report.
GPs' pay has risen sharply
Practice partners now work seven fewer hours a week on average, but earn 58% more, the National Audit Office found.
The spending watchdog said primary care trusts had not used powers to force better access for patients.
But a health minister said the contract had helped stem a "haemorrhage" of GPs from the NHS.
The contract, introduced in 2004, offered incentives for GP practices to improve quality of care.
To encourage more trainee doctors to opt for a career in general practice, it also gave GPs the opportunity to opt-out of delivering out-of-hours care.
However, while the pay of salaried GPs who are employed has increased by just 3% over two years, the average GP partner is taking home 58% more.
In many areas, said the report, the huge government investment in GP care had not delivered improved quality, and while the number of consultations carried out had increased, they had not risen as fast as the rise in funding.
On average, the number of consultations carried out by a GP had fallen, the NAO said.
"GPs are working, on average, almost seven hours less per week, and their pay has significantly increased, suggesting that individual GP productivity has reduced," said the report.
It was too early to tell if the incentives offered to GPs were actually improving care, the NAO said, although there were "moderate improvements" in areas such as asthma and diabetes.
Karen Taylor, its director of health, said that the contract was a "bad deal" for patients and taxpayers.
Edward Leigh MP, the Chairman of the House of Commons Committee of Public Accounts, which oversees the work of the NAO, said that GPs had been the "real winners".
"The Department of Health failed to cap how much of the additional funding GP partners could award themselves.
"Progress has been made in linking GPs' pay to performance, but many are simply being paid more for doing exactly the same job."
However, Dr Laurence Buckman, from the BMA, disputed this: "The entire way GPs work has changed so it's meaningless to talk about productivity in the way the NAO has done.
"GP productivity should be measured in improvements in health, not the frequency of consultations."
Alaistair Henderson, the acting director of NHS Employers, which manages the contract, said the figures used by the NAO were "misleading".
He said the £1.76bn was based on a figure suggested by the Department of Health as the minimum it would spend on primary care, and the true overspend was in the region of £406m.
"We knew it would take some time for the contract to bed in, but we have made some significant progress in the last few years and patients are seeing the benefits," he said.
Health Minister Ben Bradshaw welcomed the report, promising to study its recommendations.
"The GP contract, as the report recognises, has stemmed the haemorrhaging of GPs from the NHS and improved the quality of care for the public."
Shadow health secretary Andrew Lansley said: "The government's negotiation of the GP contract was incompetent and hopeless."