Ian Ritchie, the new chairman of the Academy of Medical Royal Colleges and Faculties in Scotland, said Dr Lauren Connelly's fatal accident and the number of junior doctors abandoning training in key frontline hospital departments showed "there is clearly something wrong" with the way the NHS currently employs and trains junior doctors.
He called on his consultant colleagues to look at their own ways of working to ensure the welfare and enthusiasm of medical graduates is protected.
Dr Connelly was killed driving home from Inverclyde Royal Hospital in Greenock seven weeks into her first job. Her father Brian later spoke out about the hours his daughter had been working in the run-up to her accident and called for an overhaul of junior doctor working arrangements.
In his first interview since taking up the post of chairman of the Scottish Academy, Mr Ritchie said: "I feel very strongly for the plight that Mr Connelly finds himself in, because I have a daughter who is a junior doctor.
"If we are working in a service where a junior doctor drives home and at least in part because of the job ends up having an accident which results in her death, as a clinician I want to be examining what it is about the way we run the service that needs to change.
"There is clearly something wrong with the way the service is delivered, and therefore we have a responsibility to look at the way we work to ensure we make things better for doctors in training."
Mr Connelly says that in the short time his daughter worked for the NHS, she was rostered to work sets of 10 days and 12 days in a row and was routinely late home. While health boards across Scotland comply with European legislation limiting junior doctors' working hours to 48 a week, they can achieve this figure by averaging hours worked over a period of six months.
Mr Ritchie said the government had gone a long way with introducing working hours restrictions, but added: "It is clear that while there is a law about working hours and the letter of the law is being adhered to, the spirit of the law isn't being followed. Junior doctors are still working long hours.
"The consequence of that is that at one extreme it may have contributed to the loss of a junior doctor's life. At the other extreme, junior doctors are questioning their career decisions and in the Scottish context are leaving Scottish medicine."
Junior doctors train to become consultants at the same time as working for the NHS and are often relied upon to cover departments at night.
However, hospitals are struggling to fill all the training slots in some fields, including emergency and acute medicine. Mr Ritchie said data showed there was no shortage of applicants for the first stage of training in these fields, but by the fourth year the numbers suggested doctors were leaving for other specialities or countries.
He said Scottish NHS research showed that trainee doctors do not like jobs with "unfeasible rotas" or poor opportunities for training. "There is a connection there," he said. "If you draw an inference from these facts, at the very least you have to examine the way we do things if for no other reason than for the future of NHS Scotland."
Asked what should happen, he said different solutions may be suitable for different medical fields but there were examples of consultants altering their work patterns to cover anti-social hours and this "excellent" practice should be shared more widely.
Mr Connelly welcomed Mr Ritchie's comments and said: "Junior doctors should not be put in a position where they work to the point of exhaustion, and patients should not be treated by exhausted staff. I hope doctors, senior medical professionals, the NHS and the Scottish Government will work together to address this very serious problem and to improve the welfare and workload of junior doctors."
A Scottish Government spokesman said: "We welcome this call from the Academy of Medical Royal Colleges and are already working with the British Medical Association (BMA) to improve our guidance, where necessary, on junior doctor working hours."
David Reid, chairman of the BMA's Scottish Junior Doctors Committee, said he had met Health Secretary Alex Neil and discussed working hours. He added: "Junior doctor rotas are a concern that we have to try and address."
The NHS has also come under fire for its weekend cover after reports the number of staff working falls by up to 60% on Saturdays and Sundays. The government said it was working to enhance weekend staffing levels to ensure patients received proper care.