Officials said that it took a couple of days for the South's Navy to seize the North Koreans as they attempted to run away after crossing into the South.
In an extremely unusual case, South Korea on Thursday deported two North Koreans after finding out they killed 16 fellow crew members on their boat then fled to South Korean waters, Seoul officials said.
"We made a decision to deport them after determining that accepting them to our society could pose a threat to the lives and safety of our people and that such criminals cannot be recognized as refugees under global law", Lee added.
Unification Ministry spokesman Lee Sang-min said: "The government chose to expel them as they had committed grave, non-political crimes such as murder and were not subject to our protection under the law". It was the South's first deportation of North Koreans through Panmunjom.
The Coast Guard rescued 60 North Koreans but there was no way to confirm they had been illegally fishing within Japan's exclusive economic zone (EEZ) - as their boat had sunk.
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Observers say the men are likely to receive heavy punishment in North Korea, including possible execution. Acting out of anger against the abusive skipper, the three accused killed him and murdered the remaining 15 to cover up their first crime, according to the minister. It said a South Korean investigation later found the two had killed 16 colleagues, including the captain.
The government also plans to send back the fishing boat of the North Koreans, a ministry official said.
Unification Minister Kim Yeon-chul said at a separate parliamentary meeting the two North Koreans once expressed their willingness to defect, but there was no consistency in their statements. -South Korean plans to hold joint air exercises next month, warning that hopes for dialogue are "on the verge of extinction".
Russian fisheries chiefs claims they have detained more than 3,000 North Korean fishermen for fishing in its territorial waters this year, up from 863 in all of 2018. In addition, the agency praised the South Korean government for its fiscal and monetary policies although it mentioned the possibility of government support for non-financial public enterprises and large household debts as negative factors on the fiscal and monetary sides, respectively.