Of the new cases, 267 were local transmissions, according to the KCDC.
Prime Minister Moon Jae In threatened the government would take "very strong and stern measures," after it emerged that a right-wing church pastor encouraged his followers to attend an anti-government protest in capital city Seoul, Yonhap reported.
On Saturday, more than 10,000 people attended the protests led by right-wing groups, despite large gatherings being banned, according to the agency.
The pastor's church has so far been linked to 193 coronavirus infections nationwide.
The authorities are concerned that the latest outbreak could increase beyond their control.
Seoul is particularly badly affected, with clusters emerging among church congregations in the city and its surroundings.
The government imposed a range of restrictions in the Seoul metropolitan area on Saturday in response to the latest spike.
Public institutions including welfare centres, libraries and museums are now to remain closed in Seoul and the neighbouring Gyeonggi province for the next two weeks.
Clubs, karaoke bars, gyms and concert halls may also be closed down again if they fail to follow protective guidelines including making lists of visitors.
Further measures include soccer and baseball league games being played behind closed doors again, after stadiums had partially reopened to fans.
South Korea has seen sporadic clusters of infection since it relaxed stricter social distancing on May 6.