Health official Yoon Taeho separately said that the person has never been listed as a virus patient in South Korea.
Describing its antivirus efforts as a "matter of national existence", North Korea earlier this year closed nearly all cross-border traffic, banned foreign tourists, and mobilized health workers to quarantine anyone with symptoms.
Some experts say North Korea was aiming to hold South Korea responsible for a virus spread and apply more pressure on its rival.
North Korea has officially admitted to its first confirmed case of COVID-19 despite media reports of cases and deaths due to the disease as far back as February.
The defector, surnamed Kim, detailed his 2017 escape from North Korea in a pair of YouTube interviews last month with another defector.
The decision was taken on Saturday at an urgent meeting of the Central Committee of the Workers' Party after a defector returned from South Korea possibly infected with COVID-19.
The defector was spotted on 19 July in the border town of Kaesong.
For several observers, the spread of the infection in North Korea threatens to stretch an already-burdened health system, which has been negatively affected by years of isolation and global sanctions imposed on Pyongyang over its nuclear weapons programme.
Yoon said the KCDC conducted virus tests on two people who had close contact with the defector, and both of them tested negative for the virus.
The defector incident has also raised concerns about possible security lapses along the 250-kilometer border that separates North and South Korea. The journey, he said, included crossing a minefield, going through barbed wire and electric fences, and swimming across the Han River.
South Korean officials have not named the person but identified a 24-year-old man, who they say fits the description and probably returned to the North recently, Yonhap news agency reported.
On Monday, Unification ministry spokesperson Yoh Sang-key told reporters that "there is a hardship on exactly grasping where the North Korean defectors are, as they - as same as ordinary ROK citizens - do not have obligation to report [to government authorities] when they leave the country".
The number of North Korean defectors reaching the South has steadily fallen in recent years, as North Korea and China tighten border controls.