The North Korean vessel was located by South Korean authorities in December 2018. Dissidents on-board the ship had planned to assassinated Kim Jong-un, the former Japanese official warned.
At the time, the incident was not widely reported as other issues had dominated including events involving a South Korean warship and a Japanese patrol aircraft.
The former chief of the Japanese Self-Defence Forces’ Joint Chiefs of Staff, Admiral Katsutoshi Kawano, told the Japanese magazine Shukan Gendai about the assassination attempt.
He explained that the ship was carrying North Korean military officers who had tried to kill Mr Kim.
He added how South Korean authorities deployed a military destroyer ship after the North had issued emergency communication.
North Korea demanded that the boat was returned but the passengers were trying to retreat from the regime after failing to kill Mr Kim.
Mr Kawano said: “Attempts by the North Korean military to assassinate Chairman Kim Jong Un in the Wonsan-Kalma region had been unsuccessful.
“Four people escaped that day and were headed to Japan by sea.”
But the South Korean ship that was later deployed became the main focus of the dispute with Japan after a Japanese aircraft flew close to the warship.
Japan insisted that the South Korean ship had targeted the Japanese aircraft with a radar.
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Mr Kim used to regularly visit the Wonsan-Kalma region were a beach resort was being built before the coronavirus pandemic began.
Earlier this month, the North Korean leader visited coastal areas which have been divested by typhoons.
He ordered 12,000 party members to join in a recovery effort and fired a party chief.
More than 1,000 houses were destroyed in coastal areas of South and North Hamgyong Provinces, according to the Korean Central News Agency (KCNA).
KCNA reported that public buildings and farmland had been flooded.
Kim Jong-un warned North Korean authorities to prepare for the dangers of the coronavirus pandemic and the typhoons.
His appearance at the party meeting towards the end of August came after widespread speculations over his health.
Mr Kim said there were “some shortcomings” in the state’s efforts to keep out the “malignant virus”, during the meeting.
North Korea has not yet confirmed any cases of the coronavirus.