The best qualified doctors are among the hardest hit by a new recruitment process which has left thousands without jobs, a campaign group claims.
Fidelio claims the future of medical research is at stake
Some 45% have yet to receive posts through the controversial MTAS system, according to a small survey of 1,300 doctors by the newly formed Fidelio.
And over 30% of those who have either a first class degree or a distinction have not received an offer, it added.
The Department of Health stressed the recruitment process was not finished.
Fidelio admitted the sample was not extensive, and that it was self-selecting.
But it said that it was the only group trying to understand the scale of the problem.
Speaking at a press conference, members warned that the future of the health service was at risk as better doctors were being overlooked in the new system in favour of the lesser qualified.
"In the long term, the quality of medical care will decline," said Professor Steve O'Rahilly, who heads Cambridge University's Department of Clinical Biochemistry.
The Medical Training Application Service, or MTAS, was introduced as part of the Modernising Medical Careers initiative aimed at cutting the number of years of training needed for doctors to reach consultant level.
It was designed to speed up the selection process, but doctors said the forms were badly worded, did not ask pertinent questions or allow them to set out relevant qualifications and experience, and had no facility for attaching a CV.
This has resulted in many doctors not being selected for their first-choice NHS trusts, and a significant number not getting any interviews at all.
Junior doctors applying to start their specialist training this year are having to compete for a limited number of training places with those who are part-way through their training under the old system.
This means that there are about 30,000 doctors chasing about 20,000 jobs.
In addition, doctors complain that while under the old, rolling system applicants had several opportunities to win a post, under the new, there was effectively only one chance.
Those who failed were being consigned to a career in the wilderness, with the prospect of becoming a specialist virtually out of the question, critics complain, as it would be another seven years before vacancies again became available.
Fidelio put forward two highly-qualified young doctors to back up its assertion that the new system, by failing to take into account the background and experience of the candidates, was missing out on some of the best.
Both Sarah and Matthew had first class degrees and "a string of awards and publications to their names", according to Fidelio.
But neither had received one of the coveted seven-year training posts.
Matthew said that no-one at his interviews had asked to read his glowing references, and that he was told his PhD did not count as a qualification, while a course in resuscitation did.
For her part, Sarah said that the questions asked at interview had nothing to do with clinical expertise or experience, but focused on issues such as "how would you cope with the workload?".
Neither however will be out of work, as both have been offered fixed term specialist training contracts - although this, they say, is a "dead end" offer.
Fidelio contacted 20,000 young doctors to take part in its poll. Of those only 1,300 chose to respond.
In addition, the recruitment process is still ongoing, as stressed by the Department of Health.
"We appreciate how stressful this process can be for junior doctors and their families. But it is important for everyone not to jump the gun. We have not even reached the end of Round One - the first stage of the process of making job offers to junior doctors," it said in a statement.
"We expect Round Two to last until 31 October. However, even then, we have asked the NHS to try to make sure that appointable junior doctors will have an educational opportunity next year."
In the second round, as many as 25% of all the jobs will once again become available as those who received more than one offer make their choice, and the posts they rejected need to be filled.
The computer system has been abandoned for this second round, which will be reliant on the more traditional CV approach.
Fidelio hopes that the training schemes will be modified to allow those on fixed term contracts to compete again further down the road with those already into their training.