Analysis by the Health and Social Care Information Centre (HSCIC) suggested practices in the poorest areas spend a smaller proportion of their income on services.
GPC deputy chairman Dr Richard Vautrey said the findings raised questions over plans to increase the deprivation weighting in the Carr-Hill funding formula.
The analysis, however, found no trend when specific groups - salaried, non-dispensing, urban practices and single-handed GPs - were analysed.
Dr Sally Hull of the Clinical Effectiveness Group (CEG) at Queen Mary University of London and a GP Jubilee Street Practice in Tower Hamlets, said those groups probably covered most of the deprived urban areas in England. She said she was concerned the analysis had not accounted for the effect of deprivation on gross income.
GPs in deprived areas have said their practices are underfunded because the funding formula does not recognise the additional workload caused by the effects of deprivation on health.
Carr-Hill is currently weighted on age and sex, meaning areas such as east London with a poor but young population may be disadvantaged.
NHS England has reportedly told GPs in east London that work to give greater weighting to deprivation could be in place by 2016/17.
The new research calculated practices’ Earnings and Expenses Ratio (EER) by Index of Multiple Deprivation score to inform the Carr-Hill review.
It found that in 2012/13 59% of the income of GPs in the most deprived decile went to expenses. For practices in the least deprived, the figure was 62.1%. When premises expenses were excluded the figures were 50.9% and 55.2%, respectively.
‘This means that in more deprived areas a lower percentage of GPs’ gross earnings are taken up by expenses,' the report said.
It added: ‘In more deprived areas a lower percentage of GPs’ gross earnings are taken up by expenses and therefore a GP is receiving, on average, a higher proportion of their earnings as income before tax.’
‘For these groups the EER of any decile is not significantly different from any of the other deciles for either year suggesting deprivation had no effect on their earnings and expenses.’
The report found average superannuable income in the most deprived quartile was £98,313, compared to £96,046 in the least deprived.
Dr Vautrey said the paper raised many questions but did not try to provide the answers. ‘Many assume that GPs working in practices in affluent areas would earn more than those in deprived areas but this paper suggests that that is not the case and is in fact the reverse’, he said.
‘It also raises questions as to whether changing the Carr-Hill formula to move more funding away from practices serving elderly populations towards those in areas with higher deprivation would necessarily achieve the aim it was intended to.’
Dr Hull said the research raised more questions than it answered and taht she was concerned the authors did not address the question on gross income in relation to deprivation.
Some variation in ratio, she said, could be reasonable if practices in deprived areas were receiving lower gross income in the first place.
Other factors such as lower labour costs in poor areas could also explain the results, she added.