Dr Fiona Cornish, president elect of the MWF, said PCTs will see the payments as ‘an easy target’ to squeeze as they try to make savings.
But she warned it was ‘short-sighted’ because it could force more women to take up salaried positions.
She said: ‘The problem is that it will be a disincentive for practices to take on women.
‘This will have a detrimental effect because if we don’t have enough partners then the service becomes weaker.’
Meanwhile, MWF president Dr Clarissa Fabre said maternity pay could be under further threat once PCTs are abolished.
She said it was unclear whether the NHS Commissioning Board or consortia would take responsibility for the payments.
But she said consortia budgets could be too tight for them to afford maternity pay.
‘When PCTs are abolished who is going to take over the maternity locum payments and are they going to pay?’ Dr Fabre said.
‘I am worried that with the new consortia these maternity locum payments could be under threat.’
Meanwhile, one Scottish health board has already taken steps to cut spending on maternity pay. NHS Ayrshire and Arran is reducing the funding for maternity leave, paternity leave and sick leave.
Paul Ardin, director of primary care development at NHS Aryshire and Arran said: ‘Under the previous scheme we allocated funding automatically to the maximum level in the Statement of Financial Entitlements.
‘The interim arrangements we currently have in place now set the level of funding on a case-by-case basis.’
NHS Ayrshire and Arran has said it will work with GPC Scotland to determine how it will provide support to GP practices to cover maternity leave, paternity leave and sick leave.