The watchdog has been called upon to consider whether health boards are meeting their full obligations under EU working-time regulations. It has also been asked to assess whether the safety of doctors - and their patients - is being put at risk by fatigue caused by working excessive hours.
The call, by Scottish Labour's health spokesman Neil Findlay, follows concerns raised by the death of a junior doctor in a road accident as she drove home after a 12-hour night shift.
Lauren Connelly, 23, was seven weeks into her first job, at Inverclyde Royal Hospital, Greenock, when she died in a crash on the M8 in September 2011.
Her father Brian Connelly believes she was suffering from fatigue built up over the previous month-and-a-half.
Glasgow University graduate Dr Connelly had worked her first 10 days in a row, including one half-day and four days of 12 hours or more, totalling 91.5 hours. She worked a 44-hour week and had a weekend off before starting a 12-day stint of more than 107 hours.
The week she died she had completed four day shifts in a row and was starting a run of seven nights back-to-back.
In a letter to the head of the HSE in Scotland, David Snowball, Mr Findlay wrote: "This really is quite shocking and reveals a culture and structure that is neither in the interests of patients nor those junior doctors who have to work such excessive hours."
He called on the HSE to investigate whether health boards were meeting their full obligations under the European Working Time Directive. Health boards comply with the regulations - which limit junior doctors' hours to 48 per week - by averaging time worked over six months.
Mr Findlay said Dr Connelly's death highlighted a "potentially very concerning situation that is quite possibly impinging on the health and safety of junior doctors".
The Lothian MSP told The Herald: "Lauren Connelly's death was tragic. Her father was brave enough to come forward and expose the reality of life as a junior doctor in Scottish hospitals and I commend him for doing so.
"I have now written to the Health and Safety Executive to ascertain whether they have looked into the issue of overworking among junior doctors and if they haven't then whether they will launch an investigation."
He added: "Working 10-hour-plus shifts for days without a break should not be tolerated in any workplace; how-ever, to ask our medical professionals who have patients' lives in their hands to do so is completely unacceptable."
A spokeswoman for the HSE said: "We will be reviewing the letter and will respond in due course."
The HSE is responsible for the enforcement of the working-time directive and can enforce limits for weekly hours, night shifts and conduct health assessments based on working times.
Mr Connelly, 61, from East Kilbride, called for an overhaul of junior doctors' hours earlier this month. He highlight-ed an "insider's guide", published by NHS Education for Scotland, the body that oversees medical training, telling newly-qualified medics to expect to be exhausted for their first month working and warning of dehydration and hunger. The booklet has since been withdrawn.
Safety expert Professor Rory O'Neill, of Stirling University, the editor of environmental health magazine Hazards, has backed Mr Connelly's call for a review of working practices, citing a 2005 US study that warned of the high risks faced by medical interns who got behind the wheel when over-tired.
First Minister Alex Salmond, who agreed to meet Mr Connelly, said junior doctors' average working hours had fallen from 58 per week in 2004 to 48 to meet the EU directive.