At present there are 34,250 doctors applying for 18,500 specialist training posts in the UK through the controversial Medical Training Application Service (MTAS).
The BMA claims that if those doctors who are unsuccessful in their application want to remain in the NHS then the option for many will be to apply to staff grade or trust grade posts, which are not accredited for training.
But, the BMA argues, ongoing delays to the contract will make these posts less appealing.
Mr Mohib Khan, chairman of the BMA SAS committee, said: "We are the last group of healthcare workers to have the opportunity to vote for a new contract. The government seems intent on delaying the contract so that the money earmarked to improve prospects for SAS doctors disappears into the black hole of NHS finances.
"The problems with training reforms, combined with the mishandling of the new SAS contract, will create a rapidly expanding group of demoralised doctors who are deeply pessimistic about their future careers in medicine. For a government intent on modernising the NHS and driving up standards, creating thousands of disaffected demoralised doctors does not seem sensible," he added.
The DoH was not immediately available for comment.
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