The comments follow the publication of a report by a DoH working group on women in medicine last week.
GPC negotiator Dr Beth McCarron-Nash told GP: 'When the model contract for salaried GPs was introduced, the GPC argued for the risk management of maternity leave being at PCO level, as we felt this risk was too high to be held at practice level.'
Under the current statement of financial entitlements (SFE), PCO maternity leave payments are discretionary. The SFE says they should pay up to £978.91 a week for the first two weeks, and £1,500 a week thereafter - usually up to 26 weeks.
Dr McCarron-Nash said: 'PCO reimbursement being discretionary means that some female GPs and practices are left significantly out of pocket.'
She added: 'PMS GPs do not have to offer the model salaried contract so may offer statutory maternity pay only, which is wholly inferior to GMS salaried GPs allowance.'
The report, Women Doctors: Making a Difference, calls for urgent modelling of the impact of 'greater female participation in general practice and the potential costs of maternity cover'.
It adds: 'Contractual changes should be considered based on this modelling.'
Dr McCarron-Nash said the GPC was keen to discuss a better maternity leave deal.
'We would urge the DoH to consider this. A start would be for maternity reimbursements to be made mandatory.'
The report also calls for the DoH to improve access to childcare and to introduce part-time medical training to improve the gender balance at the top of the medical profession.
It suggests improving access to mentoring and career advice, and says medical workforce planning should take greater account of the profession's increasingly female profile.