The data reveal a picture of rising expenses and declining income for PMS partners.
Income for partners across GMS and PMS practices rose from £105,300 on average to £105,700 over the same period.
But GMS partners saw average income rise from £99,200 to £100,400, while PMS partners' average income fell from £116,300 to £115,300.
Expenses for GMS and PMS practices rose to an average of £156,900 per partner, an increase of 2.4%. The proportion of gross earnings taken up by expenses in 2009/10 rose to 59.8% across GMS and PMS practices.
Partners at GMS non-dispensing practices saw the biggest rise in average income in 2009/10, from £95,900 to £97,300. PMS dispensing practice partners saw the greatest fall, from £132,200 to £131,100.
Average income for salaried GPs across the UK rose from £57,300 to £58,000 between 2008/9 and 2009/10.
Income for partners in England remained significantly higher than for their counterparts in the rest of the UK.
But income in England fell between 2008/9 and 2009/10, while it rose in other UK nations. Income in England fell from £109,600 to £109,400. In Scotland it rose 3.5% from £86,500 to £89,500; in Wales it rose from £90,700 to £93,500; and in Northern Ireland from £89,700 to £91,400.
NHS Information Centre chief executive Tim Straughan said: 'If we consider GP earnings over time, the average pay for a contractor GP at present is a decrease on the peak of £110,000 in 2005/6.'
The data also show huge variations in pay. A total of 6.9% of partners in PMS and GMS practices earned less than £50,000 in 2009/10. A total of 30.6% earned between £50,000 and £100,000, and 39.9% earned between £100,000 and £150,000.
Income in 2009/10 was between £150,000 and £200,000 for 9.9% of GPs and 2.7% earned more than £200,000.
GPC deputy chairman Dr Richard Vautrey said variations between PMS and GMS and partners and salaried GPs were decreasing slowly. He said part-time working by salaried GPs partly explained their lower incomes.