Dr Lewis Morrison, chair of the British Medical Association (BMA) in Scotland, said staff “need the tools to make things better”.
Instead, they have been “bearing the brunt” of what he described as “system-wide” failings which have been “letting patients down at all stages”.
In response, Health Secretary Humza Yousafs said the sector could take “years” to recover.
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Dr Morrison’s comments came as he delivered his final report to the BMA’s annual representative meeting in Edinburgh,before stepping down.
He said it had been “nothing short of a miracle” that the medical profession had come through the challenges it faced during the pandemic.
However he warned that Covid-19 has had the most profound impact on the physical and mental health of health workers – with some already being forced or considering leaving the profession.
DR Morrison said NHS staff are being left as the “messengers who bear the brunt for the myriad of things going wrong across the whole health care system”.
He added: “My message is simple – stop asking doctors to say sorry and give them tools to make things better.
“There’s an opportunity to be grasped here. If it isn’t, the medical profession and the people of Scotland will be the worse for it.”
He said GPs, receptionists and nurses are also being placed in the “firing line”, and added: “The pain of working in, and apologising for, a system that is simply letting patients down at all stages is hard to over-estimate.
“Years of underinvestment and a frankly complacent attitude to working conditions and recruitment have led us to where we are now.
“The rubber band that is our NHS was stretched so far and tightly before the pandemic that it has now snapped in many places.
“We need more honesty and frankly an explanation from the Scottish Government on how they allowed the NHS to come into a pandemic so grossly understaffed and under-resourced.”
Speaking at Leith GP surgery in Edinburgh, where he launched a recruitment drive to hire a further 800 GPs, Mr Yousaf responded: “There’s no doubt that the pandemic has been the most difficult challenge the health service has faced in its entire existence.
“GPs are the front face of that because they’re often the front door.
“But what I would say is that it’s not actually their fault. It’s not doctors’ faults or nurses’ faults. Nobody but nobody could have predicted the impact that this pandemic would have.
"We will invest, we will grow the workforce and recover as quickly as we can.
“But it will take time. And we’ve got to be upfront and honest about the fact that a recovery of the NHS is not going to happen in weeks or months.
“It is going to take years to happen.”
Sandesh Gulhane, the Scottish Conservative health spokesman and a GP, said the BMA’s comments are a “damning indictment” of the “mismanagement” of the NHS in Scotland.
“Dr Morrison identifies that heroic NHS staff are exhausted and many are quitting because they are sick of being left to carry the can for the failings of Humza Yousaf and co,” he said.