On Sunday and Monday, rain hit the capital Pyongyang and other regions, with western coastal areas reporting heavy damage.
In Anju city in South Phyongan province, officials reported 1,000 houses and buildings were destroyed and 2,300 hectares (5,680 acres) of farmland were completely covered.
The Chongchon River in Anju city flooded on Monday, cutting communication lines and submerging rice paddies and other fields, said Kim Kwang Dok, vice chairman of the Anju City People's Committee, who told The Associated Press that the disaster is the worst in the city's history.
Boats made their way through the muddy water that covered the city's streets Monday. Many residents sat on their homes' roofs and walls, watching the rising water. A young man wearing only underwear stood on a building's roof with two pigs; four women sat on another rooftop with two dogs.
Helicopters flew to various areas to rescue flood victims, state media reported. Casualties from the latest rains were not immediately reported.
If it rains again before the water drains, the damage will be greater, Kim said.
Earlier this year, North Korea mobilized soldiers and workers to pour buckets of water on parched fields, irrigate farms and repair wells as what officials described as the worst dry spell in a century gripped parts of both North and South Korea.
North Korea does not produce enough food to feed its people, and relies on limited purchases of food as well as outside donations to make up the shortfall. It also suffered a famine in the mid- and late-1990s, the FAO and World Food Program said in a special report late last year.