Payments to some GP practices have been delayed amid confusion over responsibility after PCTs were phased out in April.
NHS England admitted that some of its area teams do not have a budget for collaborative services, which include child protection reports, fostering and adoption medicals, and Mental Health Act sectioning carried out by GPs for councils.
The payments, adding up to several hundred pounds a year per practice, were PCTs' responsibility. But NHS England said funding was handed to different bodies in different areas when PCTs were abolished.
Funding, for which NHS England is now statutorily responsible, has in some areas been aligned with CCGs or local councils, causing confusion for GPs trying to obtain payment.
Birmingham LMC executive secretary Dr Robert Morley said local practices were not receiving payments until the LMC stepped in to clarify that NHS England was responsible.
Some area teams, he said, had told GPs they did not have a budget for the services. 'Whether the money is with area teams or not, they have a legal obligation to make these payments,' added Dr Morley.
Londonwide LMCs medical director Dr Tony Grewal said while there had been problems in London before April, since the implementation of NHS reforms, payments had 'disappeared down the pan'.
He added: 'The administrative functions of PCTs disappeared. No one thought about who would pay the gas bill. It's like moving house and not sorting out the utilities.'
GPC deputy chairman Dr Richard Vautrey said there should not be concerns over responsibility being handed to councils, as long as the system was consistent.
But Dr Morley said there could be 'unintended consequences', warning councils were good at 'capping spending'.
A spokesman for NHS England said it was maintaining a 'steady state' arrangement to 'avoid disruption', but would negotiate with stakeholders to 'consider how future payment levels should be determined'.
'There may be potential conflicts of interest if this responsibility was to rest with CCGs, therefore it is more likely to be a responsibility that rests with either area teams or the local authority,' he said.
Payment problems, the spokesman added, were a 'consequence of wider system issues' around GP payments.