The crew of a Maritime Safety Agency survey ship witnessed South Korean ships firing at what was reportedly a small North Korean submarine around 4:45 a.m. Friday, Transport Minister Jiro Kawasaki told reporters the same day.
It was later confirmed that South Korean ships and planes were pursuing a low-slung speedboat designed to infiltrate and extract spies, and that it was eventually destroyed.
The survey ship Tsushima was operating about 80 km southwest of Tsushima Island, Nagasaki Prefecture, when it came near the battle.
About 10 Japanese fishing boats operating in the area were ordered to evacuate, according to MSA officials.
The crew saw the South Korean military ships firing, but did not see the boat itself, MSA officials said.
The MSA dispatched four patrol vessels and an MA860 small airplane to the area as a precautionary measure and told local fishing cooperatives in Yamaguchi, Fukuoka, Nagasaki and Saga prefectures to exercise caution while operating near the area.
The Defense Agency also dispatched Maritime Self-Defense Force P-3C antisubmarine patrol aircraft and EP-3 intelligence aircraft to the area to obtain information about the incident.