The decision follows Seoul National University's move late last month to approve leave of absence requests submitted en masse in protest of the government's medical reform plans, which include increasing medical school quotas.
While reaffirming its stance that taking leave to show solidarity is not a valid reason, the ministry said its temporary measure is aimed, in part, at normalising education.
It, however, warned that students who fail to return next year will face penalties, including possible expulsion.
The ministry stressed that taking semesters off in collective protest does not "constitute legitimate grounds" for a leave of absence, but added that universities should "guarantee students the opportunity to return through individual consultation."
On September 30, Seoul National University approved leave of absence requests for the spring semester from about 780 medical students, representing around 96 percent of its total student body of the medical department.
This has raised concerns that other universities may follow suit, potentially leading to widespread absences among medical students.
A major lobby group of community doctors had renewed its demand for the government to revisit the 2025 medical school admissions quota, clouding prospects for a breakthrough to resolve months-long walkouts by junior doctors.
Choi Anna, a spokesperson for the Korea Medical Association (KMA), told reporters that the association will not join a government-organised committee tasked with estimating the medical workforce shortage, unless the government opens talks about a possible change in the 2025 medical school admissions quota.
Health Minister Cho Kyoo-hong has said it is impossible to amend the planned increase in the medical school admission quota for next year, as universities already fixed details for their enrolment plans, reports Yonhap news agency.