The five people, including four men and one woman, have expressed their wish to live in the South as defectors, the Yonhap news agency reported.
"Coast guards guided the boat to safety at (the eastern port of) Mukho," a South Korean coast guard official told AFP.
Government authorities were questioning the five North Koreans, he added.
The incident came after a North Korean fishing boat with eight people on board developed an engine trouble and drifted into South Korean waters off the country's eastern coast late last month.
Days later, South Korea repatriated all the eight, as they had requested.
Early last month, two people out of four crew members on another North Korean fishing boat which drifted to the South refused to return home. They were allowed resettle in the South.
There has also been a spate of overland border crossings in June.
Two North Korean soldiers walked across the heavily fortified border and a civilian swam across a river to defect to the South.
Over the decades since the peninsula was divided, dozens of North Korean soldiers have fled to the South through the Demilitarised Zone, which extends for two kilometers either side of the actual border.
A North Korean soldier defected to the South in September last year, and a teenage North Korean soldier defected in June 2015.
In 2012 a North Korean soldier walked unchecked through rows of electrified fencing and surveillance cameras, prompting Seoul to sack three field commanders for a security lapse.
More than 30,000 North Korean civilians have fled their homeland but it is very rare for them to cross the closely guarded inter-Korean border, which is fortified with minefields and barbed wire.
Most flee across the porous frontier with neighbouring China.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)