GPs earned an average £106,000 during the first year of their new contract, figures show.
GPs income has soared
Figures from the Information Centre for health and social care show average earnings rose by 30% during 2004-05.
Ministers and NHS bosses expressed concern that so much of the new money had apparently gone on pay, rather than on investment in services.
But the British Medical Association said doctors had "well and truly earned" their rise.
GPs who worked in dispensing practices, which have a pharmacy attached, earned an average of £128,000 after expenses - a rise of 31%.
Non-dispensing GPs earned an average of £102,000 after expenses - 30% more than in 2003-04.
The new contract, which ushered in radical changes to the delivery of primary care services, was designed to give general practices additional funds to invest in improving and developing services to patients.
It included incentives to reward GPs and their practice teams for driving up the quality of patient care.
A large proportion of GPs' earnings are now linked to the quality of care they provide, with payments made for the provision of extra services, such as contraception, child health and chronic disease clinics.
The report, which looked at income from both NHS and private sources for just under 18,000 family doctors, revealed that average total earnings for GPs was £236,000.
Tax-allowable expenses on average accounted for 55% of overall income, with GPs claiming 45% profit.
In 2003-04 GPs claimed 40% as profit, with 60% of overall income invested back into the business - 5% more than in 2004-05.
Call for investment
Health Minister Lord Warner urged doctors to invest more of their profits back into their business.
He said: "We invested extra funding in GP services in good faith both to improve services and reward GPs. The money was not intended just to boost GPs' profits.
"We expect a higher level of these profits to be invested back into their businesses, to bring about further improvements in services for patients, such as longer opening hours or widening the range of services.
"We want to see this year and next a higher proportion of practice income going on service improvement for patients, and greater efficiency rather than windfall profits."
Dr Barbara Hakin, chair of the NHS Employers' team which negotiated the new contract, said it had already started to produce benefits.
For example, in providing better information about the prevalence and treatment of common conditions and in patients starting to get access to a wider range of services in the community.
However, she said: "We are disappointed that investment in the practice-based contract seems to have resulted in such significant increases in individual GP income."
Dr Hakin said negotiations had already begun on improvements to the contract.
"We have already agreed that for 2006/07 that there would be no inflationary uplift across the contract and that general practices would need to demonstrate efficiencies, in the same way as other parts of the NHS."
Dr Hamish Meldrum, chairman of the BMA's GPs Committee, defended the big increase in pay.
He said: "Prior to the introduction of the new contract, there were serious recruitment problems and GPs¿ pay had fallen behind.
"This was officially recognised during negotiations and is reflected in pay increases under the new contract.
"On top of this GP practices worked extremely hard to deliver the Quality and Outcomes Framework targets in the new contract and have reaped the benefit, as have their patients."
Dr Meldrum added: "I believe UK general practice offers unbeatable value for money and that GPs deserve every penny of their pay."
"On average, patients see their GP about five times a year. It's a well-used service that is appreciated by patients who trust their family doctor.
"We don't discharge patients; it's potentially a lifelong partnership. And it's right that the hard work and skill of GPs is properly rewarded."