Maternity services are among several the White Paper says will be commissioned by the commissioning board when PCTs are abolished in 2013.
GPC deputy chairman Dr Richard Vautrey said 'he expects that will change' following the consultation and pressure from the GPC. 'We see no reason why (maternity) services should be treated any different to other hospital services and it is certainly something the GPC will look to change,' he added.
Delegates at an NHS Alliance workshop in London on GP commissioning expressed concern over the plans.
Dr Mark Spencer, NHS Alliance practice-based commissioning lead in the North West, said there was 'no rationale' behind the plans, which had stirred up 'strong feelings' among GPs.
As well as maternity services, the board will hold GP contracts and commission primary care, dentistry, pharmacy and a range of specialist services.
Other delegates expressed fears that the national NHS Commissioning Board would struggle to organise services to suit localities' individual needs, adding that it may struggle to intervene in local disputes effectively because of its size.
One PCT director, who asked not to be named, said he had been told there would be six regional outposts of the board, but the DoH has yet to confirm any plans for regional offices.
Dr Vautrey said the national board would 'inevitably' need regional offices to ensure it retained local knowledge.
'It's not just about maternity services,' he added. 'A massive issue is how PMS and GMS contracts are managed.
'The board structure must balance the need to be locally responsive with the need for national consistency. But it can't just be SHAs in another guise,' Dr Vautrey said.