BMA leaders expect many of the reforms, which could see GPs work longer for worse pension benefits, to be implemented as they stand.
Dr Andrew Dearden, chairman of the BMA pensions committee, warned that concerns raised during the consultation may not be taken seriously by the government.
'I suppose if I thought in two dimensions I would say that they are not going to listen to anything that we say,' he said.
Dr Dearden warned that the government 'should expect a significant backlash' from health professionals if their concerns were ignored.
He said many NHS staff had already predicted a negative outcome. 'There is a real consistency among NHS and public sector workers about what the result of the consultation will be,' he said.
NHS pensions already incorporate many of the proposed reforms, including a pension age of 65 for those joining the scheme after 2008, Dr Dearden said. 'The government wants to go to an extreme level.'
He said that by implementing reforms set out by the Hutton review, the government would damage 'a very good, stable, valued scheme which helps them'.
A Treasury spokesman said the government was discussing details of pension contributions and Hutton review proposals with health unions.
The government plans to increase public sector pension contributions by an average of 3 per cent by 2014/15, but the BMA believes doctors' contributions could rise as high as 15.5 per cent.
The Treasury spokesman said an explanation of proposed changes to pension contributions and how they will affect individual public sector workers would be published in June.
The Treasury plans to issue a 'significant report' on the Hutton review in autumn, he said.