The chairman of the British Medical Association, James Johnson, resigned from his position last night following criticism of his handling of the BMA’s response to the botched Medical Training Application System (MTAS).

Mr Johnson fell on his sword after coming under intense criticism within the BMA following the publication of a letter in the Times newspaper last week which defended the government’s chief medical officer, Sir Liam Donaldson, and the underlying principles of junior doctor training reform.

In his letter Mr Johnson, together with Professor Carol Black, chairman of the Academy of Medical Colleges, defended the government’s chief medical officer, Sir Liam Donaldson, who created the principles of the Modernising Medical Careers programme, the Department of Health’s new medical recruitment process.

David Pickersgill, treasurer of the BMA, said the letter was not in the interests of the association’s junior doctor members.

“The letter referred to the current problems over the government’s mishandling of the appointment system for junior doctors, known as MTAS. While it reflected the association’s agreed position of working towards a pragmatic solution for this year, its tone failed to reflect the anger being currently expressed by members of the association, particularly junior doctors.”

He added that the contents of the letter had led to a loss of confidence in Mr Johnson continuing in his chairman role. “It was felt to be insufficiently sensitive and has led to a loss of confidence in the chairman.

Speaking to the BBC yesterday, Mr Johnson said that at least a third of the BMA’s council were against him, and ‘things have really gone very nasty.’

He added that the investigation by the High Court of the system had left the BMA council nervous, as Remedy UK, an individual group set up by junior doctors, was fighting for their cause, whilst many felt the BMA were only interested in government negotiations.

“I think they [the BMA council] are all incredibly nervous about the effect the Remedy situation is having on the BMA. Remedy UK are very good at whipping up anger but they have no solution at all.”

The result of a judicial review of MTAS is expected on Wednesday. Department for Health legal evidence to the court have admitted that fundamental flaws with the software have been preventing it from allocating jobs to the best candidates.

The document says that the DH “could not be certain that the algorithm necessary to operate the ‘single offer system’ would be effective.”

Mr Johnson will remain as chairman of the BMA until Thursday after four years in the role. An interim chairman will be appointed shortly afterwards.

Patricia Hewitt announced that the MTAS website, has been abandoned last Tuesday, following a series of problems uncovered after the recruitment closing date.