Students in Seoul and the surrounding areas have been ordered back to online classes.
The Korea Centers for Disease Control and Prevention reported 280 new coronavirus cases as of midnight Monday, bringing the country's total to 17,945 with 310 deaths.
That represents a drop in daily new infections from 397 reported as of midnight Saturday, the highest daily tally since early March.
With most of the new cases centred in the densely populated capital area, however, health authorities say the country is on the brink of a nation-wide outbreak and have called on people to stay home and limit travel.
All students, except for high school seniors, in the cities of Seoul and Incheon and the province of Geonggi will take classes online until 11 September, the Ministry of Education said on Tuesday.
The beginning of the spring semester had been postponed several times since March, but as daily coronavirus cases dropped sharply since a February peak, most of South Korea's schools reopened in stages between May 20 and June 1.
Over the past two weeks, at least 150 students and 43 school staff have tested positive in the greater Seoul area, Education Minister Yoo Eun-hae told a briefing.
Seoul on Monday ordered masks to be worn in both indoor and outdoor public places for the first time, and has ordered places like churches, nightclubs, karaoke bars and other high-risk venues closed.


Damascus cafe blast kills 5, wounds 16
Russian air strikes kill 10, injure more than 50 in Ukraine's Kyiv
Firefighters battle wildfire in southern France
US, Iran talks conclude in Doha, focused on Strait of Hormuz
Trump honours Theodore Roosevelt in North Dakota, debuts new Air Force One
Kenyan court charges 8 schoolgirls with fellow students' murder
At least 5 people killed in fire in Antwerp apartment block
Three people die in Mexico World Cup celebrations as fans crowd streets
