The death toll remained at 256.
Battling the first major coronavirus outbreak outside China, South Korea brought infections of the virus, and the disease COVID-19 that it causes, down drastically through widespread testing, aggressive contact tracing and tracking apps.
The response has helped Asia's fourth-largest economy come to grips with the pandemic without the extensive lockdowns seen elsewhere.
The daily tally of new infections had hovered around 10 or less in recent weeks, with no or very few domestic cases over the past 10 days.
The fresh outbreak comes just as the government was easing some social distancing restrictions and moving to fully reopen schools and businesses, in a transition from intensive social distancing to "distancing in daily life".
"We must never lower our guard regarding epidemic prevention," Mr Moon said in a televised speech marking the third anniversary of his inauguration. "We are in a prolonged war. I ask everyone to comply with safety precautions and rules until the situation is over even after resuming daily lives."
He said the KCDC will get greater power as part of the long-term fight and be renamed the Disease Control and Prevention Administration to reflect its enhanced position, while the authorities beef up local expertise.
The resurgence is driven by an outbreak centred around a handful of Seoul nightclubs, which a man in his late 20s had visited before testing positive last week.
At least 24 out of the 26 new domestically transmitted infections were traced to that man, bringing the infections related to the case to 54, the KCDC said.
The KCDC said officials are tracking down about 1,900 people who have gone to the clubs, which could be increased to 7000, asking anyone who was there last week to self-isolate for 14 days and be tested.
"This case is once again showing a rapid spread of the virus as well as high infectiousness," KCDC director Jeong Eun-kyeong told a briefing. "We're in a battle against time to head off additional transmissions in the local communities."
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