GPC chairman Dr Laurence Buckman said PCTs should set up enhanced services to help practices that face five-figure losses.
'Some practices will be adversely affected; others will have their pay increase. We have to find ways to cushion them against these effects.
'PCTs in areas where lots of practices receive less due to the prevalence formula will keep the money locally - the PCT has access to that money.
'We hope they will spend that money on an enhanced service for those suffering heavy losses under the new formula.'
In 2009/10 the controversial 'square rooting' mechanism will be scrapped. The following year, pay will be weighted according to raw prevalence.
GP leaders have said some practices will lose up to five figure sums, while others will gain up to six figures. Under data protection laws, the GPC and DoH are prevented from publishing a full list of winners and losers.
GPC deputy chairman Dr Richard Vautrey assured GPs: 'No practice will go under as a result of these changes.'
Dr Buckman said he has asked the DoH to write to practices which will suffer heavy losses under the new formula, which are likely to be clustered around cities with large student populations.
An online calculator is available on the BMA website for practices in England to work out how they will fare under the new funding arrangement.
Similar calculators for Northern Ireland, Scotland and Wales will be available shortly.
- BMA prevalence calculator www.bma.org.uk
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