Laurence Slavin, a partner with specialist medical accountants Ramsay Brown and Partners, said the DoH may opt to scrap the formula as part of a move to unify GP contracts.
The GPC and NHS Employers have agreed to review the Carr-Hill formula, which weights core practice funding based on factors including the age and sex of patients, in negotiations over the next year.
GPC deputy chairman Dr Richard Vautrey has said discussions on reforming Carr-Hill were left out of this year's contract negotiations.
He said a lack of funding meant that changing the formula would have triggered a redistribution of the MPIG top-up payments brought in to protect practices from losing out when the formula was introduced in 2004.
Around 65% of GMS practices still rely on MPIG top-ups to bring their income up to the level they received before the 2004 contract, meaning their funding does not reflect Carr-Hill weighting.
Significant new funding is unlikely to be available for some time, but politicians and the GPC are keen to phase out the MPIG.
The GPC wants to remove reliance on MPIG by increasing the value of global sum payments.
Plans set out last year in the White Paper Liberating the NHS to move to a single GP contract were 'part of a drive to get rid of MPIG' according to DoH national clinical commissioning network lead for England Dr James Kingsland.
Labour shadow health secretary Andy Burnham told GP recently that the 2004 contract was a 'mistake' because of the MPIG.
Mr Slavin suggested the government may opt to scrap Carr-Hill altogether rather than continue to reform it. He said it was likely to be replaced by a 'standard pounds-per-patient formula', which could see GPs suffer 'significant' reductions in income, with some practices 'easily losing out on tens of thousands of pounds'.
'It is very unlikely that there would be any winners in this situation. The view at the centre is that GPs are overpaid, so I don't think they would have any qualms in reducing GP income,' Mr Slavin said.