The Government should have capped the amount of money family doctors can make from their practices, according to Health Secretary Patricia Hewitt.
Ms Hewitt made her statement after GPs' average pay rose above £100,000 because a new contract enabled them to make higher profits from their practices.
In an interview with the BBC, Ms Hewitt said in hindsight ministers would have wanted to ensure doctors did not make such large sums out of the new contract, introduced in 2004.
She told the broadcaster: "I think if we anticipated this business of GPs taking a higher share of income in profits we would have wanted to do something to try to ensure that the ratio of profits to the total income stayed the same and therefore more money was invested in even better services for patients.
"When we were negotiating the GP contract we had GPs taking early retirement and very large numbers of new doctors refusing to become GPs.
"Now it is quite true that neither the government or BMA anticipated how much GPs would do in response to performance-related pay.
"GPs in England are doing more for their patients in terms of prevention and giving support for long-term conditions than almost any country in the developed world."
Statistics from the NHS Information Centre show that GPs took 40% of their gross earnings in profit once expenses were taken away in 2003-4, but this rose to 45% the following year when the new contract started.
This contributed to the hike in pay GPs received, with average pay totalling £106,000 - up 30% on the year before.
Ms Hewitt added that doctors have accepted a pay freeze for this year and the criteria for performance-related pay had been made "more challenging".
The new contract, designed to give practices additional funds to invest in developing services to patients, included incentives to reward GPs and their practice teams for driving up the quality of patient care.
Doctors criticised Ms Hewitt, saying she was "denigrating" GPs.
Laurence Buckman, deputy chairman of the British Medical Associations's GPs committee, told the BBC: "Is the secretary of state saying she wishes GP practices had not performed so well on quality targets thereby improving the delivery of top quality care?
"The government signed off the contract which ties income to quality performance. She should be proud of the achievements of general practice, not denigrating doctors for delivering quality patient care."
Opposition parties said the government's poor handling of pay negotiations contributed to the deficits the health service is currently facing.
Shadow health secretary Andrew Lansley told the BBC: "The government underestimated the number of points GPs would get for treating patients which in a way is really sad because it means the government underestimated the good job that GPs do.
"For Patricia Hewitt to distance herself from the GP contract is a show of how low her own performance has sunk."
Liberal Democrat health spokesman Norman Lamb told the broadcaster: "The government has clearly made a hash of negotiating the GP pay contracts.
"It is not helpful for them to admit incompetence after the event when the problems in the NHS are already mounting. We need an urgent review into the government's approach to such pay agreements in the NHS."
A Department of Health spokesman said she was simply reiterating previous comments that neither the government nor the BMA had anticipated how much extra work GPs would do.Reuse content