A survey of 1,100 practice managers found their average income rose 2.3 per cent to £37,325 in 2010.
The survey, by the firm First Practice Management, found 3 per cent of managers are now partners at practices.
This group earn significantly more than their peers, with average income of £48,185.
Steve Morris, an analyst for First Practice Management, said most practices were continuing to meet staff income expectations despite falling GP income.
'There is a continuing squeeze on general practice finance and the days when payments from QOF and enhanced services could be regarded as extras are gone,' he said.
A number of practices are looking at staffing levels and salaries as a result of recommendations from accountants, said Mr Morris.
Despite their pay rises, for the fifth year running the amount paid to practice managers in bonuses has fallen, the survey showed. Just a quarter of practice managers received one.
Those that do receive bonuses generally are offered around £1,000, according to the survey.
Practice managers in Scotland and Northern Ireland have the lowest salaries in the UK, although this could reflect a high number of small practices.
Greater London remains the top-paying region in the UK, with managers on average earning £40,915.
GPC negotiator Dr Beth McCarron-Nash said GPs' goodwill to their staff should be applauded.
'Salaried GPs' pay has also risen by 2 per cent this year and it seems GPs are continuing to show goodwill in tough financial times.'
Dr McCarron-Nash said the GPC would be 'pushing hard' for GPs' rising expenses to be recognised in negotiations with NHS Employers.