The shortage is also impacting on trainee doctors currently employed who are having to plug the gaps, says the Royal College of Physicians
Figures show NHS Greater Glasgow and Clyde and NHS Lanarkshire were left with a combined total of 88 vacancies last month following a national recruitment programme.
NHS Lanarkshire said it was facing greater shortages of new doctors than last year, which had created "vulnerable" areas in its hospitals.
These included care for newborns and general medicine at Monklands Hospital, Airdrie, and Wishaw General.
The board said it was "actively recruiting" and additional neonatal consultants had been appointed, but described the situation as "challenging."
It said the level of cover was causing delays in assessing patients and adding time to admissions and discharges, as well as reducing out-patient clinic activity.
The board has warned that if the shortage continues, it may affect cover for patients booked in for elective procedures, due to the need to prioritise A&E services.
NHS Lanarkshire said it was working to fill vacancies with locum doctors.
The board said there were also vacancies in A&E at Hairmyres Hospital, East Kilbride, and Wishaw General, which it was filling with agency and locum staff.
NHS Greater Glasgow is also having difficulty filling junior vacancies.
A spokeswoman said: "In common with other Scottish Boards, NHS Greater Glasgow and Clyde have a number of junior doctor vacancies following this year's recruitment round.
"We are taking the necessary measures to ensure rotas are compliant and are fully committed to providing safe and sustainable medical cover for all our hospitals."
But there was a warning from Dr Neil Dewhurst, President of the Royal College of Physicians of Edinburgh.
He said: "Difficulties in filling some trainee vacancies have been reported.
"This can put great pressure on acute rotas, particularly out of hours when medical staff can be stretched very thinly.
"This can increase the potential for impacting negatively upon patient safety and reduces the quality of patient care, resulting in delayed admission and discharge.
"Doctors' training also suffers as a consequence of other trainee doctors having to plug gaps in rotas at the expense of their training.
"A Catch-22 situation can develop in which trainee doctors are reluctant to apply for positions in regions which are known to be over-stretched.
"This can exacerbate and prolong the problem."
However, NHS Lanarkshire denied there would be any impact on patient safety.
A spokeswoman said: "We have completed a substantial recruitment programme over the past 18 months and have increased consultant numbers across Lanarkshire.
"We are also actively recruiting to junior posts within general medicine.
"These vacancies do not impact on patient care. Clinicians and managers undertake daily monitoring to ensure we maintain services."
But Dumbarton MSP Jackie Baillie, Scotland's Shadow Health Secretary, said: "5000 staff have been axed and there are fewer nurses now than when the SNP came to power. None of us can be satisfied with this track record.
"The NHS in Scotland needs and deserves better."