The DoH is working on a locally determined quality framework to help overcome health inequalities.
Professor David Colin-Thome, national clinical director for primary care, said the NHS was working on the 'next phase' of the quality framework, which would address local issues.
NHS chief executive David Nicholson said the MPIG should be reformed and working in under-doctored areas incentivised.
Giving evidence to the Public Accounts Commission in parliament last week, Professor Colin-Thome claimed that the new GMS contract had improved recruitment of GPs across the UK, including under-doctored areas, but had not closed the gap in health inequalities.
Contract changes in the coming years would redress that, with incentives to work in under-doctored areas, he said.
Future contracts would also include incentives for practices to keep their patients as it becomes easier for patients to choose between GPs, he said.
Afterwards, GPC deputy chairman Dr Richard Vautrey said he was concerned about interfering with the integrity of the quality framework and 're-inventing the wheel'.
Data and treatment of conditions that affect the nation as a whole, like heart disease, would become inconsistent with local schemes, he said.
'The facility for PCTs to develop a local framework on top of the national quality framework, using enhanced services, had been in place since 2002,' he said.
Professor Colin-Thome, Mr Nicholson and Mark Britnell, director general of the NHS spent most of the session defending new GMS after the National Audit Office revealed it had cost the DoH £1.7 billion more than expected.
Mr Nicholson added that the DoH is pushing PCTs to build polyclinics because the NHS is 'fed up' with waiting for services to improve locally.
Mr Britnell rubbed salt in the wounds of GPs by referring to the BMA's recent poll to justify funding for extended hours.
'I can't find anyone who thinks extended hours is bad thing and that is why 92 per cent of GPs expressed a preference for it,' he said.
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