In a revised operating framework for 2010/11, health secretary Andrew Lansley also said all GP access and extended hours targets will be scrapped.
The document pledges that as management funding and infrastructure is stripped back, resources will be transferred to GP commissioning groups in the form of a 'running cost allowance' by 2012.
PCTs and SHAs will be expected to reduce their costs by at least £222 million in 2010/11 and a further £350 million by the end of 2011/12.
A DoH White Paper, expected at the start of July, will set out further details of how GP commissioning will work.
The GPC is calling for management-type salaries to cover GPs' time and clarity over who will be responsible for commissioning budgets.
GPC negotiator Dr Chaand Nagpaul said payment to GP commissioners should be made irrespective of the savings or losses their consortia generate.
'This should be no different to the accountability of NHS middle managers, who have a salary that is unaffected by their decisions,' he said.
National Association of Primary Care vice chairman Dr Peter Smith said GPs were 'itching to go' with commissioning but 'absolutely have to be' remunerated for all of its associated costs.
He called for full funding to cover the cost of contracting and administrative work.
Sources close to the Conservatives have speculated that money could be removed from the GP contract to pay for GP commissioning. No details have been given as to how QOF points for access targets will be redistributed.
It remains unclear whether GPs will be able to profit from the savings their consortia make.
Mr Lansley has said commissioning budgets and practice income must be kept 'wholly separate'. The GPC also opposes the idea of linking GP pay to savings generated by consortia.
Any decision to ban practices from taking a share of savings may endanger a commissioning pilot in Mr Lansley's own Cambridgeshire constituency. GPs in the area hold hard budgets and may be able to keep up to 10 per cent of savings.