The comments by Deputy Health Minister Jun Byung-wang followed remarks a day earlier by President Yoon Suk Yeol that doctors need to come up with a "unified proposal" on the appropriate increase in medical school admissions, Yonhap news agency reported.
However, Yoon said a hike of 2,000 medical students is the minimum, vowing not to back down from the number.
"The government is willing to engage in discussions with an open mind if the medical community proposes unified and more rational measures based on scientific evidence and logic while discontinuing collective action," Jun told reporters.
"We hope doctors deliver their opinion in a rational manner while protecting their patients," Jun said.
About 12,000 trainee doctors have been on strike in the form of mass resignations since February 20, with medical professors having submitted resignations in support of the walkout.
Medical professors, who are senior doctors at major hospitals, also began cutting their working hours starting Monday to cope with growing fatigue caused by a protracted walkout by junior doctors.