North Korea threatened on Friday to settle scores with South Korea over what it claims were atrocities against North Korean fishermen by the South Korean Navy.

The move came hours after South Korea repatriated three North Korean fishermen and their boat, which crossed the western maritime border due to an engine failure.

The South Korean Navy captured the fishing boat that sailed into South Korean waters Thursday evening after its repeated warnings to retreat back to the North's waters.

The South Korean Navy said it had held the North Korean ship in custody for the safety of the fishermen, considering the bad weather conditions.

Still, South Korea sent the fishermen and their boat back across the sea border in the wee hours of Friday after the North Koreans told South Korean authorities that their ship drifted due to engine problems and they wished to return to their homeland, according to South Korea's Joint Chiefs of Staff.

Meanwhile, the General Staff of North Korea's military claimed that the navy seized the fishing boat illegally by intruding into the North Korean waters on Thursday night.

North Korea does not recognize the western maritime border, which was unilaterally drawn by the U.S.-led U.N. forces at the end of the 1950-53 Korean War that ended in a cease-fire, not a peace treaty.

The area along the poorly defined border -- home to rich fishing grounds -- has been the site of several bloody clashes between the two rival Koreas.

The North's General Staff also claimed that South Korean sailors beat the fishermen with iron sticks and shackled and blindfolded them as they took the boat to Baengnyeong Island, South Korea's northernmost territory in the Yellow Sea.

"The gangsters of the South Korean navy separated our sailors and forced submission upon them with guns leveled at them on the island," an unidentified spokesman for the General Staff of the North's military said in comments carried by the North's official Korean Central News Agency.

He claimed that the North Korean fishermen have not yet come back to their senses, but "are still in coma due to the shuddering barbaric atrocities" committed by the South Korean Navy.

The North's military "will certainly force the group of gangsters of the South Korean navy to pay a dear price for their shuddering atrocities," the spokesman said, without elaborating.

Repeated calls to South Korea's JCS spokesman seeking comment went unanswered on Friday evening. (Yonhap)