Paul Gray, who became director general for health and social care and NHS Scotland chief executive at the end of last year, said he was aware concern had been raised about new medics working excessive hours and would raise it with health board chief executives.
His promise follows a campaign by Brian Connelly, the father of junior doctor Lauren Connelly, who died driving home from a night shift at Inverclyde Royal Hospital, Greenock.
Dr Connelly was seven weeks into her first job when she suffered her accident. Before Christmas Mr Connelly revealed the hours she had been working and called for an overhaul of junior doctor's working patterns.
Discussing the issue in his first interview since his appointment was announced, Mr Gray said: "If any member of the NHS in Scotland loses their life whether they are on duty or off duty, that is a tragedy in its own right. If there is something we could do to help ensure one such tragedy is prevented then I want to do that."
Since Mr Connelly began calling for change, Scottish Government representatives have repeatedly said all health boards are meeting the European Working Time Directive limiting the working hours of doctors to 48 a week. However, boards can do this by averaging working hours over six months.
The Herald submitted questions last year that revealed five boards were rostering some doctors to work more than 87 hours in a week.
Mr Connelly has said his daughter had to work up to 12 consecutive days, had no time for lunch and was routinely late home. He is calling for the European Working Time Directive to be implemented in spirit as well as on paper.
Mr Gray said he intended to talk to chief executives about the issue because he wanted to know what was happening.
He said: "I will be asking, 'What more could we be doing to assure ourselves we are not putting the wellbeing of patients or junior doctors at risk by our current approach?'"
Mr Gray, who took over the helm of the NHS following the departure of Derek Feeley last year, said he wanted to understand what the issues were and then to see what could be done.
He raised the matter on Wednesday at a meeting with health board chief executives.
Mr Connelly welcomed Mr Gray's decision to discuss the issue with senior managers. He said: "I would encourage them to seek input from junior doctors as to how things really are on the ground, the pressure they are under, and the number of hours they work in addition to those they have on rostered shifts.
"There is ample evidence from the annual junior doctors' survey that is consistent over many years in clearly demonstrating junior doctors are routinely working in excess of their rostered shifts and this is causing them to be tired as a result.
"This is bad for them and has the potential to have a detrimental impact on patient care."
The Scottish Government is already working with the British Medical Association (BMA) in Scotland to improve guidance on junior doctors working hours.
A spokeswoman for BMA Scotland, said: "We welcome Mr Gray's interest in wanting to have a better understanding of junior doctors' rotas. It is important it is not just the letter of the law, but also the spirit of the law that needs to be implemented if positive changes are to be made.
"There needs to be a greater recognition among employers of the effects of fatigue on doctors and patient safety and NHS boards need to work with junior doctors to develop rotas that are sensible and safe."