A survey of 1,100 practice managers found their average income rose 2.3% to £37,325 in 2008/9.
The survey, by the firm First Practice Management, found 3% 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.
GPC negotiator Dr Beth McCarron-Nash said GPs’ goodwill to their staff should be applauded.
'It seems GPs are passing on [generously] to their staff. Salaried GPs' pay has also risen by 2% 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.