Some lenders have refused young GPs loans, and others are imposing tougher checks before agreeing to lend.
Jeanette Brown, a partner at accountancy firm Dodd & Co, warned this may leave some retiring GPs unable to sell their share of a partnership.
Loan refusals were the first practical consequences of heavy student debt, she said. A BMA study this year found final year students had an average debt of £22,821 (GP, 15 April).
Ms Brown said in recent months she had advised two young GPs who hoped to buy into a practice but struggled to secure bank loans.
One bank asked for profit projections to be demonstrated, which she said was unprecedented in her experience.
'While many banks are still open for business as far as doctors are concerned, new partners may find their requests for buy-in loans turned down if they already have a combination of student loans, credit card debt and large mortgages,' Ms Brown said. 'It is a common misconception that only low earners get into financial difficulties.'
GPC chairman Dr Laurence Buckman said the situation was likely to worsen. 'It's inevitable that young doctors starting out with debt won't be able to take on a bigger debt,' he said.
'It was always predicted that putting junior doctors at the moment of qualification into debt would cause problems. Charging for hospital accommodation for student doctors only makes that worse.'
Dr Buckman said little could be done to alleviate the situation, but it was likely that it 'would sort itself out'.
'This is little consolation to doctors struggling to buy into practices and GPs wanting to be bought out,' he said.