Confederation chief executive Gill Morgan said Mr Johnson had redefined the relationship of the BMA with government as constructive rather than obstructive, and believed its influence could wane without him.
'The relationship with the Department of Health is fragile and if Mr Johnson's resignation causes the BMA to move to pointing out problems rather than helping work out solutions, it would significantly weaken the influencing position of the BMA,' she said.
'A future chair may find themself hamstrung to the detriment of doctors and the medical profession if they can't have a thought without running it through the committees.
'It will become very slow and would make the chair job very difficult. The BMA urgently needs to think about the role of the chair.'
NHS Alliance chair Dr Michael Dixon warned that recent improvements in clinical engagement could be hit by Mr Johnson's departure.
He said a 'historic alienation' between the DoH, government and doctors had produced 'an angry front line', and he called on the new BMA chair to continue Mr Johnson's bridge-building role.
'A new BMA chair could reflect the anger of the front line, which has led it to get the post in the first place. But we need to look at the next step, not reflect on the past,' he said.
Hospital Consultants and Specialists Association chief executive Stephen Campion said it was a shame Mr Johnson was the 'only one to fall on his sword'.
'He has been a casualty of a bigger problem and there needs to be greater accountability at the DoH.
'It is part of ministerial duty to ensure the implementation of policy and somebody needs to be accountable for the failure,' he said.
Mr Johnson, who chaired the BMA for four years, said he had not intended to seek re-election for a fifth and final year of office in elections in June. He said his early resignation had been 'precipitated by unhappiness within the association', because of a letter he co-wrote to The Times (see 'How MTAS spelled the end for Johnson', below).
BMA treasurer Dr David Pickersgill said it was this letter that sealed Mr Johnson's fate.
'Its tone failed to reflect the anger currently being expressed by members of the association, particularly junior doctors,' he said. 'It was felt to be insufficiently sensitive and has led to a loss of confidence in the chair.'
Academy of Medical Royal Colleges chair Dame Carol Black, who co-wrote the letter with Mr Johnson, told HSJ she was surprised by the anger it had provoked.
Matt Jameson Evans of doctors' pressure group Remedy UK said he did not regard Mr Johnson's resignation as a victory, and said it was a 'terrible situation' for the BMA to be in.
The BMA is now considering whether to accelerate the election of a chair ahead of its annual representative meeting in June or to introduce interim arrangements.
By convention, the BMA chair is alternated between hospital doctors and GPs, so it is expected that Mr Johnson, a vascular surgeon, will be succeeded by a GP.
BMA GP committee chair Dr Hamish Meldrum and deputy chair Dr Sam Everington are considered favourites for the post.
How MTAS spelled the end for Johnson
The controversial selection system for trainee hospital consultants that prompted Mr Johnson's resignation has been drastically scaled down amid mounting anger from junior doctors.
Health secretary Patricia Hewitt announced last week that the medical training application service (MTAS) will no longer be used to recruit junior doctors.
After the first round of recruitment, applications for specialist training posts will now be overseen locally by medical deaneries.
Mr Johnson co-wrote a letter to The Times, with Academy of Medical Royal Colleges chair Dame Carol Black, rejecting a proposal by junior doctors to abandon the MTAS scheme including the first recruitment round.
Although this reflected the BMA's agreed position, anger among the profession meant Mr Johnson felt he had no option than to resign.
Police are investigating last month's MTAS security breaches, when applicants' personal details could be seen online by the public