Dr Brian Keighley, chairman of the British Medical Association (BMA), said the Scottish Government's unwillingness to mitigate the impact of a UK Government decision to take more money from doctors' pay to put towards their pensions has "severely damaged trust amongst the medical profession".
His comments came after the union's UK council decided last month not to proceed with strike action after a ballot of hospital doctors in Scotland.
While 73% of junior doctors and 52% of staff and associate specialists who voted in the ballot said they were willing to take strike action, the BMA said the overall level of support in the ballot was insufficient to mount effective action.
The BMA has previously warned trust in Holyrood ministers was undermined as a result of the changes to the NHS pension scheme.
Dr Keighley said: "This has been a really challenging year for the medical profession.
"Doctors' decisions to even consider taking industrial action, up to and including a strike, reflects badly on any Government. Scottish ministers must recognise the dispute over pensions has severely damaged trust amongst the medical profession.
"Continued attacks on doctors' terms and conditions have had a serious impact on workforce morale as doctors face a further year of pay freezes, increases to their pension contributions, at the same time as meeting rising demand for services.
"There is only so much goodwill in the profession and at the moment it is severely strained.
"If Scottish ministers wish to continue the journey towards a quality NHS responsive to patients' needs, they will soon have to re-engage with the medical profession it has treated so badly in 2012. However, there are some encouraging signs that the Scottish Government is willing to listen."
Dr Keighley added: "I hope that, as we enter 2013, the Cabinet Secretary Alex Neil recognises the burden of the NHS pressures that are falling on the shoulders of the workforce and looks to develop policies that support the workforce."
A Scottish Government spokeswoman said: "Doctors play a crucial role in looking after our patients every day of the year, and we continue to work closely with the BMA on issues affecting its members.
"In particular, reaching a negotiated settlement for the GP contract for next year will bring real benefits to patients, with GPs working more closely to help those patients most at risk of hospital admission.
"We continue to be actively involved in pension discussions with the BMA and other NHS trade unions, and we will continue to work in partnership with them to find a way forward on pensions issues within the ever tighter constraints imposed on us by Westminster."