The average UK GP partner earned £105,300 before tax in 2008/9, a fall of around 0.7 per cent on the previous year.
Although gross earnings have risen by 2.6 per cent, expenses leapt by 5.1 per cent.
Accountants say a hike in heating and power costs, and rising sessional GP and nurse salaries, have caused the rise.
The average income for salaried GPs in the UK rose to £57,300 in 2008/9, an increase of 2.7 per cent on 2007/8.
Laurence Slavin, partner at specialist medical accountants Ramsay Brown and Partners, said QOF had increased stationery costs. 'GPs are writing more often to their patients and we have seen costs increase significantly,' he said.
Mr Slavin said the first year of extended hours increased costs as GPs open longer and pay staff extra.
Many GPs say enhanced services funding did not cover their costs, he added.
GPC chairman Dr Laurence Buckman said the DoH must recognise GPs face financial pressure in a number of areas.
The GPC hopes to agree funding for the time GPs will spend on commissioning under planned NHS reforms, but is not seeking to profit from this.
The number of GPs with an income above £250,000 has remained at about 250 (0.8 per cent) since 2005/6, despite media claims they are becoming more widespread.
Profit per partner has fallen by around 4 per cent since its peak in 2005/6 of £110,000.
GPs in England earn £109,600 on average, but GPs in Northern Ireland and Wales earn much less, with average incomes in 2008/9 of £89,700 and £90,700 respectively.