The GPC has been notified that some practices were not paying locums within a 10-week time frame.
Primary care organisations (PCOs) can decide not to allow pension contributions sent outside the 10-week limit, but some PCOs are stricter than others, the GPC has said.
While locum GPs would not be forced to opt out of the NHS pension scheme as a whole in this circumstance, they would lose out on pension benefits for that specific piece of work.
The GPC urged practices to pay locum GPs within 10 weeks, and 'preferably much earlier'.
GPC deputy chairman Dr Richard Vautrey suggested this is unlikely to be a widespread issue, and said there was no reason why practices should delay paying locums.
He said: 'Practices have a professional obligation to follow best practice. I would encourage practices to do the right thing with regard to locums, and it's down to the individual practices to ensure this happens.'
He warned that practices failing to pay within 10 days may find it more difficult to secure locums in the future.