The warning comes as NHS chief executive Sir David Nicholson said that the DoH may force consortia to share back-office functions as management costs are slashed.
Administrative funding for GP consortia, public health, the NHS Commissioning Board and the regulator Monitor will total less than 5 per cent of the NHS budget, Sir David told a health select committee enquiry last week. He said spending on administration would be cut, but refuted a claim that it currently accounts for 14 per cent of NHS funds.
DoH's arms-length bodies will share back-office functions and GP consortia may be forced to do the same, he said.
'We haven't made a decision on how much freedom GPs will have,' he said.
David Stout, director of the NHS Confederation's PCT Network, said when funding is split between the NHS Commissioning Board and local authorities, it would leave 'not very much at all' for consortia.
Barbara Hakin, DoH director of commissioning development, said 'most' of GP consortia's management allowance would be spent on freeing up GPs from clinical duties. Ms Hakin also refused to rule out PCT debts being passed onto consortia.
The exact amount GP consortia will receive per patient for managerial costs is due to be published in December.