Lynne Abbess, head of primary care at specialist law firm Hempsons, said how the government handles existing PCT deficits could make a 'significant difference' to whether GPs want to become partners.
If substantial PCT deficits transfer to consortia, practices in the area may find it harder to turn a profit, she warned.
The White Paper Liberating the NHS set out plans to pay a 'quality premium' to consortia if they manage finances well.
But this is likely to be funded from existing GP income.
'If the quality premium is top sliced from GP remuneration and paid to consortia, where a consortium is unable to afford to pay it back to GPs how is that going to leave the practice?' Ms Abbess said.
'If the quality premium is a significant percentage of the income stream it could leave them in difficulty, depending upon the margin of profitability. This could influence a doctor's desire to become a principal,' she added.
'We have seen in the past (before the 2004 GMS contract) the reluctance of some GPs to take on liability by becoming a partner. Even the most entrepreneurial would be fools to join up to a consortium which carries a huge debt that is largely outside its control in the first year of operation,' Ms Abbess said.
The DoH has not ruled out consortia taking on PCT debt, but said the matter was up for discussion during the consultation period (GP, 20 August).
GPC deputy chairman Dr Richard Vautrey said: 'I think the key element is what proportion of GP income the quality premium is. Many GPs have local enhanced service deals that link resources to referral and prescribing, so it could be nothing more than that. Until we have seen the details we should keep an open mind.'