By Agence France-Presse
"A small boat was spotted in waters off the north of Baengnyeong Island" near the inter-Korean border, the source told Yonhap news agency, adding that the officer, who holds the rank of major, and a civilian were aboard the vessel.
"They expressed willingness to defect," he said.
A Korea Coast Guard official said relevant authorities were investigating the case, declining to give details.
The defection was the 14th involving a North Korean soldier since 2000.
The last defection by a North Korean military officer took place in 2008, YTN TV said.
It is the first defection by any North Korean since a historic summit between the two Koreas which saw their leaders agree to pursue the denuclearization of the peninsula and a permanent peace.
In November last year, a North Korean soldier drove to the heavily-guarded border at speed and ran across under a hail of bullets from his own side.
He was hit multiple times in the dramatic defection at Panmunjom truce village.
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.
In June last year, two of four crew members on a North Korean fishing boat which drifted to the South refused to return home and they were allowed resettle in the South.
A month later, five North Koreans in another small boat crossed the sea border into South Korean waters and expressed their wish to live in the South.
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.