Mr Johnson, a vascular surgeon at Halton Hospital in Runcorn, stood down on Sunday after nearly four years at the helm of the BMA.
The letter, published on 17 May and co-signed by chairman of the Academy of Medical Royal Colleges Dame Carol Black, backed both the recommendations of the MTAS review group and CMO for England Sir Liam Donaldson, responsible for MTAS.
It rejected a suggestion favoured by junior doctors at that time that a first round of interviews under MTAS be scrapped.
In the letter, Mr Johnson admitted to faults in the much-derided £1.9 million MTAS system designed to help sift through the new draft of junior doctor applications. But he said that, while there were glitches that needed to be ironed out, it should not be scrapped altogether.
In the letter, Mr Johnson wrote: 'We restate our support for the CMO and his role in improving junior doctors' training. He pioneered the principles underlying the reform programme.
'It would be a shame if those principles were obscured by recent problems with the online application system.'
Mr Johnson's comments, which lost him the confidence of colleagues on the BMA council, enraged junior doctors who bombarded the BMA with more than 500 telephone calls over the weekend.
BMA treasurer Dr David Pickersgill said Mr Johnson's comments were insensitive.
He added: 'While the letter reflected the BMA's agreed position of working towards a pragmatic solution for this year, its tone failed to reflect the anger of members of the BMA.'
The letter attracted a barrage of complaints to Times Online from doctors who said he had failed to stand up to ministers on their behalf.
The MTAS system was scrapped last week for the second round of interviews, which will now rely on a CV and covering letter system. Results of the first round stand. The result of a judicial review into MTAS was expected this week.
Mr Johnson had told colleagues he did not intend to stand for re-election when his term in office ends next month. A new chairman will be elected next month.
Contenders for BMA chairman
DR HAMISH MELDRUM - Dr Meldrum has been the chairman of the GPC since July 2004. The PMS GP and former East Yorkshire LMC chairman is also an RCGP observer.
DR SAM EVERINGTON - Renowned for his holistic approach to medicine, Dr Everington is deputy chairman, and now acting chairman of the BMA. Dr Everington has acted as an official health advisor to government ministers and was a founding member of the Commission for Health Improvement.
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