Due to changes brought in as part of Modernising Medical Careers, 50 per cent more specialist training posts have had to be filled this month compared with last August.
The new process saw 32,600 applicants applying for 20,000 training scheme places across Britain.
The failure of the computerised Medical Training Application Service led to delays in matching trainees to posts and there were still around 1,000 vacancies as HSJ went to press.
The problems have sparked fears of widespread service disruption.
British Medical Association consultants committee chairman Dr Ian Wilson said: 'Operations and clinics will have to be postponed.'
However, the Department of Health and NHS Employers have insisted that trusts will cope.