GP leaders have admitted prevalence winners could see their gains undermined by cuts to enhanced services.
Practices with high disease prevalence will see their income rise from April with the removal of the square rooting mechanism that damps pay weighting for quality framework points. It will rise further when the system changes again in April 2010.
The overhaul will mean that primary care organisations (PCOs) in areas with high disease prevalence will pay practices hundreds of thousands of pounds more than they do now.
The increases have been heralded as finally recognising fully the extra workload faced by practices in high prevalence parts of the UK.
But the funding shifts will be met from within PCOs' existing budgets, because quality framework pay is not redistributed nationally.
As a result, GPC chairman Dr Laurence Buckman said that where PCTs are paying out more on prevalence, enhanced services cuts are possible.
'There is a potential risk that those PCOs are going to have to find money from their own budgets. Enhanced services will be a challenge this year. I suspect (trusts in high prevalence areas) will not want to pay out.'
John Ford, head of health policy at the BMA, said there was extra pressure on PCOs because their budget allocations are independent of the GP contract.
Mr Ford said it was 'unfortunate' that there was no mechanism to truly redistribute prevalence funding nationally.
'The SHA could top up funding in theory I suppose, but there is no mechanism to distribute funds nationally. I don't think the government would like that anyway, as it goes against its policy of localism.'
Meanwhile NHS Employers has written to PCTs in England warning of the destabilising effect prevalence changes will have on practices that lose out.
Mr Ford said the DoH may offer no more than 'general encouragement' for PCOs to provide support for such practices.
The GPC hopes local enhanced services can be negotiated to compensate practices.
But Dr Buckman warned: 'Obviously there won't be pound for pound compensation. Some people who lose will lose, and that is fair.'
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