Vice Health Minister Park Min-soo told a briefing the physicians risk having their medical licenses suspended if they do not return to hospitals.
He added that as of Wednesday (February 28) only 294 of the more than 9,000 trainee doctors are back at work.
Two-thirds of the country's junior doctors have walked off the job to protest government plans to increase the number of students admitted to medical school.
The plan aims to boost numbers of physicians by 2,000 each year to address what the government says is a shortage of doctors.
But the doctors themselves say pay and working conditions should be addressed first.
The strike has caused huge disruptions at major hospitals which have been forced to turn away patients and cancel surgeries.
Junior doctors are a crucial for South Korea's highly-regarded medical system, making up 40% of staff at large teaching hospitals.
An alliance of groups representing patients suffering severe illnesses called on doctors to return to work on Thursday so there can be discussions on how to improve the medical system for everyone.
Kim Sung-joo is an esophageal cancer patient.
"There are news reports about the delayed treatment of patients, and the fact that this situation could drag on is deeply disheartening and frustrating for patients in severe conditions and their family members who rely on surgery or cancer treatments. Due to the reality of a medical vacuum, there is no alternatives."
25-year old junior doctor Ryu Ok Hada says trainee doctors work more than 100 hours a week, making between $1,500 to some $3,000 a month, including overtime pay.
"I wanted to become a doctor because I want to stand next to the people when they are at their most vulnerable, when they're lonely and in pain. For this reason, I decided to work at the emergency center. However, the government is only pressuring trainee doctors unilaterally, without dialogue, and threatening to arrest us."
South Korean President Yoon Suk Yeol vowed on Tuesday to go ahead with the plan and said there was no justification for the protests this reform had triggered.
The government was due to meet with the trainee doctors on Thursday in a bid to persuade them to return to hospitals.
There have been no formal discussions as of yet.
The government says the Korean Medical Association, which represents mostly private practitioners, was not the right body to address the trainee doctors' concerns.
