The wooden vessel crossed the Northern Limit Line in the East Sea, also known as the Sea of Japan, at about 11:20 pm Saturday.
Seoul: A North Korean boat with three crewmen crossed the de facto maritime border with South Korean and has been towed to a port, Yonhap news agency reported on Sunday, citing the South's Joint Chiefs.
The wooden vessel crossed the Northern Limit Line in the East Sea, also known as the Sea of Japan, at about 11:20 pm Saturday, Seoul's Joint Chiefs of Staff said, according to Yonhap.
The crew and their boat were taken to a South Korean military port for investigation, it said.
It was not immediately known whether they were defectors or accidentally crossed the border.
In June a fishing boat from North Korea carrying four men managed to cross the intensely monitored sea between the countries and dock undetected. Two of the men were sent back to the North and the other two said they wished to defect.
A South Korean general was sacked over the lapse in border security.
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 land border, which is fortified with minefields and barbed wire.
Most flee across the porous frontier with neighbouring China.