A controversial new recruitment system for junior doctors is to be reviewed amid claims the whole process is "fatally flawed".

Doctors and consultants - some in Scotland - have suggested some of the most able candidates have not been shortlisted for interviews.

Now the Department of Health has launched an inquiry amid concern that qualifications and achievements have not been sufficiently taken into account during shortlisting and that candidates have not been rated in a consistent fashion.

The review follows an emergency meeting between Secretary of State Patricia Hewitt and leading UK doctors who have raised a number of concerns about the new system.

Last year The Herald highlighted fears among doctors that they could be posted anywhere in Scotland under the new regime and that many people would be left outside the mainstream training programme and struggle to further their careers.

As concerns grew, doctors in England mounted a campaign calling for the introduction of the new process to be postponed.

The allegations that staff without the right qualifications were being invited to shortlist interviews were made last month as the British Medication Association warned the actual applications machinery had descended into pandemonium with computer problems.

This week a panel of consultants in Birmingham refused to conduct job interviews on the grounds they were unfair.

Yesterday the association said this Medical Training Application Service (MTAS) was fatally flawed.

It is the way MTAS has operated which will now be reviewed, with Westminster promising the process will be complete before the application system enters its second phase next month - when doctors are offered posts and others enter a clearing system where they apply for remaining vacancies.

Professor Neil Douglas, president of the Royal College of Physicians of Edinburgh, is to lead a working group which is overseeing the review.

He said: "It is clear that MTAS has caused confusion and concern to many doctors throughout the UK. I am pleased that the department of health has recognised the severity of the situation and has ordered an immediate review to identify what went wrong and to ensure that such mistakes are not made again. It is clear that lessons will have to be learned from this experience if we are to restore professional confidence in this system."

Under the old training system doctors who had completed their first years in hospital following university would progress through a series of training grades by applying for different advertised posts as they worked their way towards qualifying as a consultant.

The new system centralises entry into a more concentrated training programme. Candidates can apply to join a finite number of training programmes in different medical fields and different geographical regions. Around 30,000 junior doctors have applied for 22,000 training places UK-wide following the shake-up.

Concern has been mounting about the way the system has operated with representatives from the Royal College of Physicians and Surgeons of Glasgow (RCPSG) saying they had "lost all confidence in the process."

Dr Paul Knight, registrar with the RCPSG, said: "While the evidence at this stage is anecdotal, the reports consistently show serious problems with the system.

"We are frustrated because we raised many of these issues with the department of health and were given constant reassurance that the system would be fit for purpose. This is very evidently not the case."

Dr Graeme Eunson, chair of the BMA's Scottish Junior Doctors Committee, said most of the problems reported in Scotland were related to trainees who had applied for jobs in England. He said there were three specialist areas, gastroenterology, anaesthesia and emergency medicine where issues with candidate selection had been flagged up in Scotland. The body in charge of the process up here, he said, had decided to interview all applicants to these programmes because of this.

The health department said the terms of reference for the review were "to understand what has worked and not worked to date, identify and promote good practice, recommend action to remedy any weaknesses, taking account of legal and operational constraints and identify specifically what further action or guidance is required."