The government has given in to protests from the medical profession over a controversial new system to select young doctors for specialist training.
Junior doctors will have a right to appeal
The British Medical Association (BMA) said the system was badly organised, failed to draw out expertise and could not cope with demand.
Initial findings of an independent review have now revealed the process has "shortcomings" and should change.
Health minister Lord Hunt has apologised to those affected.
He told the BBC's The World Tonight: "I'm certainly very sorry if junior doctors have been affected adversely in this way and that's why, when it became apparent from the meetings that we had with doctors early in the week, we set up this review."
He said the Department of Health (DoH) had been working "very hard" with the medical royal colleges and the BMA to deal with "the key problems" of the system.
"I know that this has been a difficult time for junior doctors and I hope that this reassures them that we have listened to their concerns," he said.
The DoH had rejected calls from the BMA to suspend the current round of interviews for specialist training posts, which began this week.
But it went on to order a review of the system after consultants threatened to boycott the interviews, claiming the system was flawed and unfair.
In a statement, the DoH said there will now be "significant" changes to the second round of interviews, which is due to begin in April.
This will include allowing applicants to provide CVs and portfolios to support their applications. At present no CV can be included with an application form.
In addition, there will be changes to the application form and the scoring system, as well as better support and feedback for candidates.
The DoH said: "The department has accepted the need for change and the revised approach will now be tested with junior doctors, selectors, deanery recruitment teams and employers."
Those who have already been refused will be able to have their applications reconsidered.
The new system was designed to speed up the progress of doctors' training 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 is the point at which a doctor would select to focus on an area of expertise, such as cancer medicine or paediatrics.
Around 30,000 applicants are chasing 22,000 available jobs.
In addition, doctors who were applying for training posts online also faced problems with the computer systems which meant many well-qualified candidates were not offered interviews.
Anil Ghosh, a junior doctor from Oxfordshire, told the BBC's The World Tonight that the changes were a step in the right direction.
But he added: "I still think that, although in reality we are being given a second chance or a half chance of reapplying, that the system is not particularly fair as they are still not interviewing the best candidates in the first place."
The final report of the review, chaired by Professor Neil Douglas, vice-president of the Academy of Medical Royal Colleges, will be published by the end of the month.