Just six out of 21 posts for on-the-job training in emergency medicine have been taken at the end of the annual recruitment round.
Acute medicine departments, which treat the rising number of frail elderly patients sent to hospital, are also struggling to secure new talent. Out of 22 vacancies, only nine (41 per cent) are now filled.
The Scottish Government has already ordered the empty posts to be advertised overseas.
Publicity about the vacancies has been specifically targeted at Australia, Canada and the United States. The closing date for applications is tomorrow but officials say they are not expecting huge interest.
The problem is not unique to Scottish hospitals, with only 29 per cent of senior emergency-medicine training vacancies filled UK-wide. Acute medicine is a little better across the UK, at 58 per cent.
Junior doctors specialising in emergency and acute medicine at this level have already spent a number of years working in hospitals since graduation and are relied on to look after patients, particularly during evening and weekend shifts.
Dr David Reid, chairman of the British Medical Association's Scottish Junior Doctors Committee, said: "Increasingly, while trainees want to have further training programmes, they also want to spend time with their friends and family. Emergency and acute medicine rotas are quite demanding and do not address work-life balance as much as they should."
He said it was reasonable to consider offering incentives or enhanced contracts to doctors in these fields to recognise the onerous shift patterns, adding that negotiations about building such flexibility into junior doctor contracts were currently taking place.
It is not the first year that frontline hospital services have struggled to attract enough senior trainees in Scotland, although the problem appears to be increasing. In 2011, 62 per cent of emergency training vacancies and 76 per cent of acute medicine vacancies were filled.
Dr Reid said: "It is a vicious cycle. When you have a system that's somewhat under pressure, such as unscheduled care, and you are not filling 100 per cent of the jobs, it is going to add to the pressures that are already in the system."
Neil Findlay, Scottish Labour's health spokesman, said: "The failure to attract enough junior doctors is a real crisis for our NHS.
"There is absolutely no way that this won't impact on patient care or heap pressure on to existing staff, who are already overstretched as a result of the SNP's mismanagement of the health service."
The Herald has been running a campaign, Time for Action, calling for a review of capacity in both the NHS and social care, including the number of doctors, as part of a plan to prepare services to cope with the growing elderly population.
NHS Education for Scotland (NES), which oversees junior doctor recruitment, launched a drive last year to ensure Scottish medical jobs were attractive to young medics across the UK. This included revamping its website, using social media and attending a careers fair in London.
Anne Dickson, general manager for training at NES, said it tackled "a lot of myths" about being a junior doctor in Scotland such as: "If I apply to Scotland they could post me anywhere (in the country)" or "Scotland does not give you opportunities".
Health boards with vacancies can employ locums on short-term contracts to fill any gaps, and there may be a second recruitment round in the autumn.
A Scottish Government spokeswoman said: "Fill rates for medical trainee posts in Scotland remains at a high level, and in some cases are better than elsewhere in the UK. While there are some issues recruiting in a limited number of specialities, this issue is not unique to Scotland, and we are working closely with NHS boards to support their staff recruitment efforts.
"This government is leading the way in improving the working lives and working hours of junior doctors, and recently announced steps to reduce the pressures and long working hours experienced by junior doctors."