Blackwater Valley and Hart and North Hampshire PCTs are considering stopping the locum payments from April.
North East Hampshire LMC chairman Dr Stephen Linton said: 'The key part of this is maternity cover. Maternity leave is 26 weeks and full-time locum cover costs about £2,000 a week, so it will cost practices £52,000.
This is sex discriminatory and, I think, a breach of the contract.'
The GMS statement of financial entitlement states that PCTs 'must provide financial assistance' to a maximum of £978.91 per week, although how much is discretionary.
GPC deputy chairman Dr Laurence Buckman said PCTs had to pay something under the contract, but he admitted that it could be as little as 1p.