Practices that struggle to recruit long-term staff could face a five- figure annual rise in costs for every GP post they fill with a locum.
Under UK government plans for the 2013/14 GMS contract, GP practices in England and Wales will take responsibility for paying 14% employer superannuation for locums.
The payments are currently made by primary care organisations.
GPC pensions subcommittee chairman Dr David Bailey said it was expected that a fixed payment would be added to practices' global sums to pay for locum superannuation.
A GMS practice of average size in England or Wales will receive around £1,500. Funding will be weighted by list size but will not account for the number of locums employed.
Funding for the 40% of practices in England on locally negotiated PMS contracts has yet to be determined.
Dr Bailey warned that small practices and practices in under-doctored areas could be hit by a 'significant' rise in costs. A small practice in Wales with 2,000 patients will receive around £600 a year, he said.
'That would pay for around 10 days of locum cover. Most people like to take six weeks of holiday and people get sick,' he said.
Dr Bailey said practices in under-doctored areas could lose out if they had to employ a number of locums over a year.
The total cost of superannuation for locum GPs hired to fill a full-time post over one year could be £15,600, far more than the £1,500 a year the average practice will receive.
'The costs will fall on the poor practice which can't recruit somebody on a regular basis,' Dr Bailey said.
Practices that pay locum insurance to cover partners' sick leave could see a 14% rise in fees to cover the superannuation costs, he added.
He said the BMA would urge the DH to delay the plans by at least a year.
Russell Finn, client principal at specialist medical accountants Ramsay Brown & Partners, said the changes could cut both partners' and locums' pay.
A DH spokeswoman said: 'Our proposals are intended to make sure the payment arrangements are fair to GP practices. Current PCT expenditure on this will be shared equally between practices in the future.'