Around half of the surgeries scheduled at 15 major hospitals have been cancelled since last week, according to the health ministry.
Under South Korean law, doctors are restricted from striking.
Earlier this week, the government requested police investigate people connected to the stoppage.
Seoul’s police confirmed that it raided the Korean Medical Association (KMA) on Friday.
In response to the Thursday deadline and initiation of a police probe, the KMA slammed the government for “intimidation tactics” and accused it of turning the country into a “totalitarian state”.
The government says it is trying to address one of the lowest doctor-to-population ratios among developed nations. It is pushing to admit 2,000 more students to medical schools annually from next year.
Doctors say the plan will hurt the quality of service and medical education, but proponents say medics are mainly concerned the changes could erode their salaries and social status.
The KMA said its members will hold a rally in Seoul on Sunday, with local reports saying around 25,000 expected to join.