National Association of Primary Care president Dr James Kingsland said most PCTs are carrying out a complete review of PMS contracts, which could see PMS practices forced back to GMS deals.
Dr Kingsland said the reviews may bring a 'substantial reduction' in PMS practices in 2010/11. Around 40 per cent of practices in England are currently PMS.
GPC deputy chairman Dr Richard Vautrey warned this would create a 'big problem' as PMS practices moving to GMS would have no right to MPIG protection.
'For the majority of PMS practices this would deliver a significant resource cut in the region of tens of thousands of pounds, which would destabilise practices and the services they provide,' he said.
Dr Vautrey called for a 'sufficient' rise in the global sum to ensure it was financially possible for PMS practices to move to GMS contracts.
Dr Kingsland suggested PMS practices that have difficulty demonstrating their added value will be the most at risk.
'Where there isn't a big difference between GMS and PMS contracts, it will be hard to justify why PMS practices are getting extra funding,' he said.
But Dr Kingsland called PCTs' approach 'rudimentary' and 'unfair', and suggested their actions did not align with world class commissioning.
'If PCTs are now saying PMS practices are over-funded then that is the failing of the PCT in the first place, as they agreed the contract,' he said. 'I would also question why they are only realising this now.'
He warned that PMS contracts should not be seen as a 'cash cow to go and raid' in times of financial difficulty.
'PMS contracts should have a strong future, but it is in the hands of PCTs becoming world class commissioners,' he said.