The General Medical Council (GMC) has told health officials to look at complaints including a warning that a staff shortage at NHS Lothian at weekends is "dangerous".
The issues, logged by 230 trainee medics following a national survey, are said to be being treated "very seriously" by NHS Education for Scotland (NES).
Among the concerns cited was a lack of senior doctors in hospitals at weekends and being unable to access vital diagnostic services, such as scans.
At some hospitals, there is just one senior doctor to 100 beds at weekends.
Junior doctors at St John's Hospital in Livingston, West Lothian, described weekend cover as "very poor", adding: "Genuinely believe this is unsafe and do not think it is fair that we are put in this position to work this shift."
Death rates are rising by up to 27% at some hospitals in England, but in Scotland the same level of data is not available, prompting calls for NHS boards to be more transparent.
"Patients have a right to know this information," said Margaret Watt, who is chairwoman of the Scotland Patients Association (SPA).
Niall Dickson, chief executive of the GMC, said: "It is vital that doctors in training can raise concerns if they are worried in any way about safety and that when they do they are listened to and their concerns addressed."
A spokeswoman for NHS Education for Scotland said: "NES takes this very seriously and undertakes a rigorous investigation of every concern. We are working with NHS boards to which these concerns relate and will report to the GMC."
A Scottish Government spokesman said: "Safety is a seven day a week, 24 hour a day responsibility.
"We have no evidence in Scotland that admission is less safe on a particular day of the week from any other.
"Surgical outcomes, including mortality, vary for a large number of reasons – severity of illness, unscheduled surgery, underlying health conditions of patients, and so on.
"Surgery is complex and it is not as simple as dividing results by day of the week.
"We are not complacent and that's why we have a workstream in Scottish Patient Safety Programme dedicated to making procedures safer for everyone – whatever day of the week they are admitted."