Most cases were in and around Daegu, the country's fourth-largest city, where the flu-like virus has spread rapidly through members of a fringe Christian group.
Health officials expect the number of new cases to be high for the near future as they complete the testing of more than 200,000 members of the sect, as well as thousands of other suspected cases from smaller clusters.
"We need special measures in times of emergency," South Korean Prime Minister Chung Sye-kyun told a cabinet meeting, referring to extra medical resources for hotspots and economic measures including a $9.8 billion stimulus.
"In order to overcome COVID-19 as quickly as possible and minimise the impact on the economy, it is necessary to proactively inject all available resources."
COVID-19 is the illness caused by the new coronavirus which emerged from China late last year to spread around the world.
Hospitals in South Korea's hardest hit areas were scrambling to accommodate the surge in new patients.
In Daegu, 2,300 people were waiting to be admitted to hospitals and temporary medical facilities, Vice Health Minister Kim Gang-lip said. A 100-bed military hospital that had been handling many of the most serious cases was due to have 200 additional beds available by Thursday, he added.
South Korean President Moon Jae-in on Tuesday declared "war" on the virus, apologised for shortages of face masks and promised support for virus-hit small businesses in Asia's fourth-biggest economy.
Moon's office on Wednesday said he had cancelled a planned trip to the United Arab Emirates, Egypt and Turkey in mid-March due to the crisis.
At least 92 countries have imposed some form of entry restrictions on arrivals from South Korea, according to a tally by Yonhap news agency.
Vice Foreign Minister Cho Sei-young met the US ambassador on Wednesday as part of Seoul's efforts to prevent the United States from imposing restrictions.
In the meeting, Cho outlined South Korea's efforts to control the outbreak and urged the United States not to take steps that would affect exchanges between the two countries, the foreign ministry said.
US President Donald Trump said this week his administration was watching Italy, South Korea and Japan - all with severe outbreaks - and would make a decision about travel restrictions "at the right time".
"We remain confident in the South Korean government’s robust and comprehensive response efforts to limit the spread of the virus," US ambassador Harry Harris tweeted after meeting Cho.
Up to 10,000 people are being tested each day in South Korea, and daily totals have decreased slightly since a peak of 909 new cases on Saturday, the KCDC said.
Experts caution that the results of those tests could take some time to be processed, leading to future spikes in confirmed cases.