The Department of Health is to carry out a review of the new system to select doctors for specialist training.
Many junior doctors are chasing posts
The move follows a decision by a group of top consultants to boycott the process.
The consultants, from the West Midlands, said they would not interview any candidates, claiming the system was flawed and unfair.
The British Medical Association said the current round of interviews should be suspended.
The Department of Health refused this request - but did agree to a review.
It will be completed by the end of March, so that any changes deemed necessary can be put in place before a second round of recruitment begins in late April.
This will allow doctors not granted an interview in the current round a second chance.
Doctors' training was revamped in 2005, with the aim of speeding up progress so juniors could reach consultant level in an average of 11 years, rather than the current 14.
However, doctors who have been through their initial stage of training under both the old and the new systems are all competing for a limited number of specialist training posts this year.
As a result the BMA says over 28,000 UK doctors are currently competing for 22,000 posts.
The BMA said the new system set up to process applications was badly organised, failed to draw out applicants' expertise and could not cope with demand.
It said there was growing evidence that able doctors had not been offered any interviews.
It also claimed that non-medically qualified staff were involved in the recruitment process, while consultants had insufficient time to shortlist applicants fairly.
A computer system set up to deal with the recruitment process crashed after being overwhelmed by the number of applications.
The West Midlands consultants had been due to select candidates to work in general surgery.
In a statement they objected to the fact that a longlist of candidates had not been drawn up prior to the selection panel, and said the new system had been rushed in to meet an unrealistic deadline.
They said: "We owe it to our patients and the profession that we are able to select and appoint the best candidates to surgical training posts and felt strongly that this was impossible today."
They said the decision had been explained to the candidates, who were supportive.
Meanwhile, the BMA wrote to Health Secretary Patricia Hewitt, warning the continued failure of the government to act could have disastrous consequences for both doctors and patients.
Dr Jo Hilborne, chairman of the BMA Junior Doctors Committee, welcomed the review.
But she said: "Not only is this response, too late, it also does not go far enough.
"The only fair solution now is for the interview process to be suspended until it can be clearly shown that no doctor has been disadvantaged as a result of the government's mistakes."
Lord Hunt, the health minister, denied doctors had been unfairly treated, and said many would have another chance to apply successfully.
"This system was designed with a huge input from doctors themselves. It did emphasise practical skills and competencies.
"Let me assure you that in the first round of appointments, only the candidates of very good quality will be appointed.
"There is then to be a second round starting in April, and there will be many more places, many more people will be shortlisted, and the second round will of course be informed by the review which is going led to be the medical royal colleges."
Andrew Lansley, the Shadow Health Secretary, said: "The government has waited until thousands of junior doctors were in despair about their career before they understood the need for action.
"They have badly mishandled the recruitment process."