Income for partners across GMS and PMS practices rose slightly 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 greatest 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, the data show.
Income for partners in England remained significantly higher than for their counterparts in the rest of the UK. But income in England fell slightly between 2008/9 and 2009/10, while it rose by up to 3.5% in other UK countries.
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 it rose from £89,700 to £91,400.
NHS Information Centre chief executive Tim Straughan said: ‘Our report shows that, on average, a GP working in the UK earned roughly the same pay before tax in 2009/10 as they did in the previous year.
‘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 between GP partners. 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.
A DoH spokesman said: 'We are committed to securing the best possible value healthcare from the GP contract so that resources are used to the greatest benefit for patients and the taxpayer.
'The average GP income is now £4,200 (3.7%) lower than in 2005/6. In addition, all public sector staff earning more than £21,000 a year, including GPs, are subject to a two-year pay freeze in 2011/12 and 2012/13. The GP contract changes recently agreed with the BMA recognises this and demonstrates commitment to delivering improved patient care.'