SHAs were instructed by the DoH to start separating the commissioning and provision of medical education in England by April this year.
Dr Michelle Drage, joint chief executive of Londonwide LMCs, said this will effectively mean NHS managers controlling how GPs are taught, rather than deaneries.
'If you split the functions then the deanery will end up with one or none of these roles. If the commissioners are not medical commissioners, they will be SHA commissioners.
'Training then becomes driven not by what makes the best GP, but what is best for managers and their services.'
Encouraging competition between deaneries could lead to some being starved of funds, said Dr Drage.
'It is theoretically possible that some could end up going bust,' she said.
Dr Prit Chahal, chairman of the UK Association of Programme Directors (UKAPD, formerly the UK Association of Course Organisers) said encouraging competition between deaneries 'may have the reverse effect on the quality of GP training.'
'I suspect this is a manifestation of the DoH's obsession with "splits" and performance indicators, in the hope that costs will be driven down,' he said.
UKAPD vice-chairman, Dr Brad Cheek, said it raised the possibility of private companies providing GP training.
'I do not think that a commercial provider would be prepared to accept the huge range of trainees currently entering GP training and to guarantee their successful completion in three years,' he said.
Dr Richard Wakeford, a UKAPD executive member, said the 'biggest issue' was whether the new coalition government would proceed with the policy. Training posts are already being frozen by SHAs, he said.
The DoH was unavailable to comment due to the recent change of government.
NHS London said the reforms would 'ensure we have the right training for the right services', and that GP educationalists were being consulted.