The British Medical Association (BMA) has summoned the health secretary Patricia Hewitt to an urgent meeting over the future of 10,000 junior doctors.
NHS Employers believe 10,000 more junior doctors are chasing training contracts than there are places and the BMA has raised concerns that half of unsuccessful applicants could leave the UK.
The BMA asked junior doctors for their plans if their application through the "flawed" medical training application services (MTAS) is unsuccessful. In the first round of MTAS 34,250 doctors are chasing 18,500 posts.
More than half said they planned to complete their training overseas, depriving the health service of their skills for at least five years. Some 4.5 per cent of these already had a confirmed overseas training post. The remaining junior doctors admitted they would leave medicine entirely.
Jo Hilborne, chair of the BMA's Junior Doctors Committee, warned the NHS could lose thousands of young doctors because of poor planning.
"This is not acceptable. It's unfair on them, it's unfair on their patients, and it's unfair on the taxpayers who've funded their training," she said.
Ms Hilborne continued: "These changes have caused anxiety on a massive scale, and we are concerned about their impact on patient care as well as doctors' morale. We want to discuss ways of addressing this with the health secretary."
However, the Department of Health (DoH) maintained that the BMA's concerns are exaggerated, adding that is it not unusual for young doctors to work or travel abroad, and the majority who do so return to the UK to continue their careers within the NHS.
A DoH spokesperson continued: "Specialty training posts in the UK are very highly skilled, so there will always be competition for these posts but these are only training posts, and there are still jobs in the NHS for junior doctors who don't get a training place.
"We want our doctors to progress and develop their careers in the NHS where we see them as our doctors of the future. There are many options open to applicants who do not secure a training place, including trust grade posts in the NHS, locum work, or spending a period of time working outside the NHS."
MPs will discuss training reforms in the House of Commons today as part of an opposition day debate. The BMA has written to all MPs outlining its concerns.
Ahead of the debate the shadow health secretary Andrew Lansley will host a meeting with Remedy UK, which represents junior doctors. The Conservatives warn "the future of the NHS is at stake" and call for an urgent solution.
Meanwhile, health workers yesterday threatened a "summer of discontent" in the NHS. Delegates at the public sector union Unison's conference criticised the 2.5 per cent staged pay rise, which they claim amounts to a pay cut.
Unison leaders are calling for a meeting with the chancellor Gordon Brown and warn of strike action unless the pay award is reviewed.