The first public admission of Covid infections highlights the potential for a major crisis in a country that has refused to accept international help with vaccination and shut down its borders.
As of March, no cases of Covid-19 have been reported, according to the World Health Organization, and there is no official record of any North Koreans having been vaccinated.
"There has been the biggest emergency incident in the country, with a hole in our emergency quarantine front, that has been kept safely over the past two years and three months since February 2020," official KCNA news agency said, referring to detected cases of a subvariant of the highly transmissible Omicron virus, also known as BA.2.
The report said people in Pyongyang had contracted the Omicron variant, without providing details on case numbers or possible sources of infection. The samples of the infected people were collected on 8 May, it said.
The report was published as North Korean leader Kim Jong Un chaired a Workers' Party meeting to discuss responses to the first outbreak of the coronavirus.
Kim ordered all cities and counties of the country to "strictly lock down" their regions to prevent the spread of the coronavirus and said emergency reserve medical supplies would be mobilised, according to KCNA.
"The state epidemic prevention work shall be switched over to the maximum emergency epidemic prevention system," KCNA said.
Although the North has never before confirmed even a single coronavirus infection in the country, officials in South Korea and the United States have cast doubts, especially as cases of the Omicron variant were widely reported in neighbouring South Korea and China.
The isolated North has enforced strict quarantine measures, including border lockdowns, since the pandemic began in early 2020. In July that year, Kim declared an emergency and imposed a lockdown on Kaesong, near the inter-Korean border, for three weeks after a man who defected to the South in 2017 returned to the city showing coronavirus symptoms.
According to the latest data from the World Health Organization (WHO), 64,207 of North Korea's more than 24.7 million people received Covid-19 testing; all had been found negative as of 31 March.
North Korea has declined shipments of vaccine from the Covax global Covid-19 vaccine-sharing programme and the Sinovac Biotech vaccine from China, suggesting no civilians may have been vaccinated.
South Korea's presidential office told Reuters that President Yoon Suk-yeol, who was sworn in on 10 May, will continue separating humanitarian aid from the political situation, opening the door to provide support to the North.
Thursday's KCNA report said Kim told the Workers' Party meeting that the latest emergency quarantine system's purpose is to stably control and manage the spread of the coronavirus and quickly heal infected people to eliminate the source of transmission in the shortest period.
The fact that Kim called a party politburo meeting at dawn and state media immediately published the deliberation shows the urgency of the situation, said Professor Yang Moo-jin of the University of North Korean Studies in Seoul.
"Externally, there may be an indirect message of the need for cooperating with the international community if it proves to be difficult to overcome on its own," Yang added.
A South Korea-based website that monitors activities in Pyongyang said this week that residents have been told to return home and remain indoors because of a "national problem" without offering details.
Earlier on Thursday, Chinese state television reported North Korea has required its people to stay at home since 11 May as many of them have "suspected flu symptoms", without referring to Covid-19.
The main crossing between China's Dandong and the north-western North Korean town of Sinuiju was closed in April because of the Covid situation in the Chinese city, China said.