One hospital, the Asan Medical Center in Seoul, put up a sign saying its emergency unit was only handling cardiac arrest cases. The emergency departments at the other four hospitals were also on "red alert", according to a government bulletin, meaning they were running out of beds.
"It is so frustrating that the resident doctors' strike is happening now," the brother of a cancer patient who had spent 10 hours looking for a hospital bed told newspaper JoongAng Ilbo.
The health ministry says 7,813 doctors have left their jobs since protests began this week over a plan by the government to increase the number of medical students to boost healthcare staffing in remote areas and meet the demands of one of the world's most rapidly ageing societies.
The government wants to increase the number of medical students to 5,000 from the 2025 academic year from 3,000 now, and then add 10,000 more by 2035.
The protesters, however, say South Korea has enough doctors, and that the government needs to address working conditions and pay, particularly in key areas such as paediatrics and emergency medicine, before recruiting more students.
South Korea's population of 52 million had 2.6 doctors per 1,000 people in 2022, far below the average of 3.7 for peers in the Organisation for Economic Co-operation and Development (OECD), and polls show many Koreans support the government plan.
One group participating in the protest called the plan a political ploy ahead of a general election in April.
"We couldn't just sit back and watch medical policies built only for the sake of winning the general election," the Korea Interns and Residents Association said in a statement.
Local media said between a third and a half of scheduled surgeries at the five major hospitals have been cancelled due to the walkout.
The protests have continued despite a government order for the doctors to return to work. On Wednesday, Vice health minister Park Min-soo urged the protesters to prioritise patients over collective action.
"The basic calling of medical professionals is to protect the health and lives of the people, and any group action that threatens that cannot be justified," he told reporters.
Safety Minister Lee Sang-min later threatened the protest leaders with possible arrest. "The police and the prosecutors' office will consult and take measures against any group or individuals who are leading collective action, including arrest and investigation," he said.
About 76% of South Koreans back the government's plan to increase the number of medical students, a Gallup Korea poll showed last week, amid concerns over staff shortages outside the greater Seoul area.
