Tuesday saw a three-digit increase in cases for a fifth day after weeks with numbers generally around the 40s.
South Korea is viewed as one of the world's coronavirus success stories for its management of the disease.
But a spike in new cases linked mostly to a church has sparked concerns of a wider outbreak.
The country recorded 246 new infections on Tuesday, bringing the nationwide total to 15,761.
Many of the new cases have been linked to the Sarang Jeil Church, whose pastor has been a vocal critic of President Moon Jae-in.