Under the 2009/10 deal, any pay rise is to be distributed in several phases according to an agreed ratio. Estimates show some practices could receive a core pay rise of up to 11 per cent from a 2 per cent national rise.
Each phase of the funding distribution process cuts cash from correction factors and recycles it into global sums.
But GP leaders in Northern Ireland fear the province's government may implement only the first step of the pay rise, and then retain money that should be recycled into the next phase.
A pay rise of 2 per cent would see an initial uplift of 2.13 per cent to all global sums. If the process stopped at this stage in Northern Ireland, a practice with an average global sum of £300,000 and no correction factor would receive £6,390, compared with up to £33,000 for an equivalent practice in the rest of the UK.
Across Northern Ireland, hundreds of thousands of pounds would be lost to GPs, fewer practices would be lifted off MPIG, and overall reduction of correction factors would be limited.
GPC negotiator Dr Richard Vautrey told the conference in Fermanagh on Sunday: 'There has been a suggestion in Northern Ireland that further savings need to be made. But this goes against the four-nation deal.'
Southern LMC chairman Dr Theo Nugent, chairman of this year's Northern Ireland LMCs conference, said: 'In the short term it would mean a loss of cash to the profession.
'But the bigger issue is if England, Scotland and Wales proceed with one structure and Northern Ireland uses another, this would set an unacceptable precedent. It would erode GP funding in Northern Ireland.'
Northern Ireland GPC chairman Dr Brian Dunn said the fears had arisen because of pressure on departments in the province to make 3 per cent annual efficiency savings. He said there had been suggestions the GP pay rise might be an easy target.
'We have told the health dep-artment that we expect the same as everyone else in the UK.'
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