Some GPs are earning as much as £250,000 a year after expenses under their new contract, the BBC has found.
Experts say the government got its sums wrong in the contract
GP wages have risen by up to 25% since the contracts were introduced in 2004, according to specialist accounts.
The figures come from an annual survey by the Association of Independent Specialist Medical Accountants due out later this month.
Experts have said the contract was ill devised and is partly responsible for current NHS deficits.
The results of the survey of earnings suggest the average annual income for GPs could rise to £120,000 before tax.
But the figures also give evidence that some GPs are earning up to £250,000.
GPs, however, say only a tiny minority earn that much. They argue their income had to be boosted, as it had fallen below that of other comparable professionals.
One accountancy firm in the north-east of England said it has just under 10 GPs earning between £200,000 and £250,000 a year.
The survey is the first of its kind since the GP contract came into effect between April and December 2004.
Policy experts have said the government miscalculated its sums when it negotiated the deal.
The Department of Health has confirmed the current overspend on GPs is £300m.
Dr Prit Buttar, a GP in Abingdon in Oxfordshire, told the BBC Radio 4's Today programme that the new contract was proving to be very lucrative.
The partners in his 10,000-patient practice now earn in excess of £100,000 a year after expenses - a rise of around 20%.
He said, for instance, his practice now received funds for monitoring cholesterol and blood pressure levels of patients with heart disease.
"It is something that we were doing already. There are elements of it where it is frankly bean-counting for its own sake - and I don't think anybody would pretend otherwise."
However, Dr Hamish Meldrum, lead GP negotiator for the British Medical Association, told the BBC average GP earnings were a bit below £100,000 a year.
He said the new contract was needed because GPs' earnings had fallen below those of other comparable professionals.
Dr Meldrum said some GPs were earning more money because they were now running a complex business.
He said: "The government has been encouraging GPs to expand to run super surgeries to grow bigger.
"There will be a few GPs who are at the top of these and primarily they are getting that sort of money for actually running quite a complex business rather than necessarily providing health care."
Tony Blair defended big pay rises for GPs and nurses.
He said: "When people say why have you spent so much on nurses and doctors' pay, I say because it's right we make our GPs the best paid in Europe, and boost nurses' pay and conditions, which is why the number of doctors in training is up over 68%, and nurses by 67%."
Patricia Hewitt, the Health Secretary, said GP pay was now tied to the work they actually did, rather than the size of their patient list.
"There are thousands of people who are alive and well today as a direct result of this new contract.
"This is an enormous improvement in health care, and it is the kind of preventive health care that the public want."
But she said: "I would be very surprised if there were a lot of GPs earning £250,000 purely from the NHS."
Niall Dickson, from the independent health think tank the King's Fund, said patients were unlikely to support huge pay increases for GPs.
"All the suggestions are that GPs are being paid more money, but overall we have not seen a big increase in productivity, indeed we may have seen a down in productivity because of shut surgeries on Saturday mornings, and no responsibility for 24 hour cover.
"It does not look like a terribly good deal at the moment for the taxpayer and the patient."
Joyce Robins, of the pressure group Patient Concern, said the BMA had struck a splendid deal for its members.
"GPs are now paid piece-meal, a few thousand for reaching this target, a few thousand for that. It has created an atmosphere where it seems that every time a GP picks up a pen or looks at a computer, it must have a price tag."