The running of doctors’ training must be taken out of the hands of the Department of Health after its chaotic mismanagement of funding and job applications, an influential report will say today.

The report by Sir John Tooke, ordered last year after thousands of highly qualified junior doctors were left without training posts, recommends that the Government be stripped of control of postgraduate medical training.

Instead, it recommends that the cash needed to train the next generation of specialists should be ring-fenced to prevent the NHS from spending it on something else, and managed by a new body, to be called NHS Medical Education England.

The recommendations, seen by The Times, are expected to be made today by the inquiry, which was set up by the department last year after a series of failures. Incidents included thousands more doctors applying for posts than were available, and problems with a computer system designed to shortlist applicants, which resulted in severely underqualified doctors turning up for job interviews.

Sir John Tooke, Dean of the Peninsula School of Medicine in Plymouth, was asked to chair an inquiry into what to do next. His interim report was published in October, and has been overwhelmingly backed by doctors. His final report, out today, is a stunning vote of no confidence in the department. Last year’s crisis “could and should” have been predicted, he told The Times yesterday. The appointments system that failed was “rushed and poorly planned”.

There are two important changes to the interim report’s recommendations. One is the formation of NHS Medical Education England, which Sir John and his colleagues say will be able to articulate the principles of postgraduate training and implement it successfully — something that the department “is in no way capable of doing”, he said. The report also gives warning that training could suffer when the European Working Time Directive comes fully into force next year.

The limit on doctors’ working hours will mean that there is not enough time to train them to the skill levels needed, he cautioned. A way needs to be found in which doctors can continue to work legally more than 48 hours a week — perhaps by separating work on the wards from training time.

But the most urgent problem is one that Sir John cannot solve — making sure that last year’s debacle over training appointments, when 30,000 junior doctors applied for 20,000 posts, is not repeated. The evidence is that the pressure on places will be more intense this year, with about three applicants for every training place, and 20 to 1 in the more popular specialties.

Sir John said that the Government had failed to reconcile two of its policies: expanding medical school places in Britain and the “open door” policy towards graduates from overseas. Unless further training places were made available this year, he said, British graduates would be disadvantaged compared with those of earlier years.

There will be a bulge in applications for higher training, caused by a growing number of British graduates, applications from those who won only a one-year post last year, and the uncontrolled number of applicants from abroad.

Last week, the British Medical Association gave warning that the process could go as badly as it did last year. Applications opened on Saturday for training posts in England that start in August this year.

Ram Moorthy, chairman of the BMA junior doctors committee, said: “Our concern is that without adequate planning, the levels of competition could result in a lottery.”

Sir John said that unless changes were made to protect the rights of British-trained doctors to at least one year of postgraduate training, a situation could arise in which students graduate from medical school but could not practise as doctors because they had not completed their year in hospital.

What went wrong

— The computer designed to shortlist applicants failed

— Consultants asked to interview applicants walked out because many of those whom they saw were unfit to be shortlisted

— At least 10,000 overseas doctors applied for posts, even though the Government had expanded medical schools in Britain to make the country self-sufficient in doctors

— Attempts by the Government to stanch the foreign applications failed in court

— The computer failure made personal details of doctors’ applications, including in some cases sexual orientation, accessible to outsiders

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