The health secretary, Patricia Hewitt, has apologised to junior doctor applicants after the problems experienced by the online system used to select doctors came under heavy scrutiny.

The Medical Training Application Service (MTAS) was repeatedly delayed with the website falling over due to demand, causing data loss and glitches to filing applications, resulting in two extensions to the original application deadline.

Speaking yesterday (3 April) to BBC Radio 4, Hewitt said: “There’s been terrible anxiety which shouldn’t have happened to junior doctors. The new system of Modernising Medical Careers (MMC) I think everybody supports but the actual implementation in this first year of transition was nowhere near what it should have been.”

Hewitt’s apology comes as an analysis of figures on the MTAS website www.mtas.nhs.uk by the BMA revealed that there are only 18,518 positions available for UK specialty training posts, with an estimated 32,000 applicants being offered interviews.

Candidates were made to fill in a form using the online service based on a series of questions.

Dr Jo Hilborne, chairman of the BMA Junior Doctors Committee, said: “Not only has the government failed to design a fair recruitment process, they’ve also misled everyone on the number of jobs available. Even if the application system improves, thousands of doctors are going to find themselves without a training post in August.

“We really don’t want highly qualified medical staff to be forced to leave the NHS, but if they can’t complete their training in this country, it could be their only option.”

Last weekend, the head of MMC, Professor Alan Crockard, resigned over the chaos caused by the introduction of MTAS.

Doctors expressed concerns that the forms were badly worded, did not ask pertinent questions or allow candidates to set out relevant qualifications and experience, and had no facility for attaching a CV, resulting in fears that the best candidates would not necessarily be selected.

Hewitt said: “We are still in the process of ensuring that every junior doctor gets an interview and those interviews have already started – but they haven’t finished – for the job of their first choice. The shortlisting process didn’t work. We are in the process of sorting it out and we are now guaranteeing every junior doctor an interview for the speciality of their choice.”

The BMA have pledged to help all applicants and are preparing to publish guidance in early May covering options available, counselling and advice services and opportunities to work overseas.

Dr Tom Dolphin, deputy chairman of the BMA Junior Doctors Committee, said: “It’s a terrible waste of talent and public money but the government’s failure to plan the NHS workforce means that thousands of UK doctors aren’t going to get opportunities to train to become GPs and consultants. At the moment there is very little in the way of a safety net for them. We’re anticipating a huge upsurge in demand for our counselling and careers advice services.”