A survey by the association of around 900 junior doctors found more than half were struggling with their workload and 41 per cent said it was potentially compromising their performance.
Stress, pressure and long hours are taking their toll on junior doctors, sometimes to the point of suicide.
Speaking at the launch of the Australian Medical Association's Junior Doctors' Health and Wellbeing Survey yesterday, AMA president Rosanna Capolingua said, ''We have been touched by the experience of having colleagues junior doctors commit suicide.
''Then there are cases where [junior doctors] have car accidents driving home after long shifts at work.
''There are things that occur that really raise the alarm bells.''
Dr Capolingua called on governments to urgently increase the number of junior doctors working in the public health system because more than half of the survey's respondents reported struggling with excessive workloads. More than 40 per cent believed this potentially compromised the quality of care they provided.
The study of 914 doctors at the beginning of their careers in medicine was taken to provide a snapshot of the health and wellbeing of these doctors and assess how well they were coping with the pressure of balancing work, study and family commitments.
Doctors nationwide and in New Zealand took part in the confidential, online, self-reporting questionnaire. Most respondents were 26-35 years old and 2 per cent worked in the Australian Capital Territory.
Nearly one-third surveyed reported regularly working ''unsafe'' hours and half had worked an average of 50 or more hours a week in the previous year.
According to the survey, more than half were at risk of compassion fatigue and 69 per cent were at risk of job burnout.
Most relied on family, friends, informal peer support and debriefing as coping strategies, a minority (3.8 per cent of males and 1.9 per cent of females) turned to alcohol. But, in spite of everything, 98 per cent of respondents said they would continue their careers in medicine and 77 per cent had enjoyed working as a doctor over the previous year.
However, 17 per cent said that, given their time again, they would not choose a career in medicine.
Dr Rosanna Capolingua noted the results reflect the pressures of an overstretched health system.
"They've got pressure on them," she said.
"It's difficult for them to manage patients if there isn't a bed for them to go into, if there's an overflow in the emergency department, if someone's surgery is cancelled or delayed.
"They're feeling the pressures that the system is creating."
Dr Capolingua says it reaffirms the need for greater healthcare funding.
The chairwoman of the AMA Council of Doctors-in-training, Alex Markwell, said the statistic that was the most interesting was that 71 per cent of those surveyed were concerned about their own health.
''For a long time doctors have been seen as superhuman or not having the same needs as other people.
''We are hoping to encourage doctors to seek health care, have their own GP and look after themselves better.''
Rehabilitation registrar at Canberra Hospital Harry Eeman agreed with many of the survey's findings.
''I have got back up in my area of medicine, but I know my more junior colleagues face those day to day stresses,'' Dr Eeman said.
''For a hospital to run well, you can't run at 100 per cent all of the time.
''There's no slack in the system: it's always at breaking point.''
Canberra's troubled health system was driving junior doctors away.
''Canberra [Hospital] and Calvary [Hospital] have the potential of being great places, but we're having a brain drain to the big cities.''