Vice health minister Park Min-soo said more than 9,000 trainee doctors had walked off their jobs so far.
The number amounts to more than two thirds of the country's resident and intern doctors, who are protesting a government plan to increase medical school admissions by 2,000 each year.
"Starting in March, it's inevitable that those who do not return will face at least a three-month suspension of licences and other legal procedures," Park told a briefing.
The walkout has disrupted hospital operations and services, with some emergency rooms turning away patients and surgeries being postponed.
