The GMC could have to charge doctors who are unable to find a responsible officer (RO) to link with for revalidation.
The council anticipates 'several thousand' doctors, mostly locums, having to pay for its revalidation services.
Locums who work for agencies without an RO could have to link direct with the GMC - and pay its fees.
The council says it is too early to say how much doctors would have to pay, but admits that 'the resource implications would be considerable'.
Under current plans for England, all doctors will link with a single RO who will advise the GMC to pass or fail the doctor's application to revalidate.
But locums who work for agencies without an RO look set to fall through the net. The legal, financial and administrative workload may deter agencies from appointing an RO, the GMC points out.
'The principle of every licensed doctor relating to a single local RO is not one that can be meaningfully sustained in practice,' the GMC says in its response to a DoH consultation that closed last week.
Doctors without ROs may have to send revalidation evidence 'direct and unmediated, to the GMC' it says. The GMC response adds: 'We have statutory powers that would enable us to charge a fee for revalidating doctors in these circumstances.'
But National Association of Sessional GPs chairman Dr Richard Fieldhouse said locums should have access to the RO at the trust whose performers list they were on.
He said the GMC response seemed to assume locums worked for a single agency, but this was rarely the case.
'Has anyone at the GMC actually sat down with a locum and asked them what the situation is? This seems a little out of touch.'