"We used diplomatic channels to demand that South Korea explain the course followed by the research vessel and strongly protested as unacceptable activities carried out without our consent," he told reporters at a briefing.
Japanese authorities said the ship was spotted near the Takeshima islands, called Tokto in South Korea, on August 1-2. It refused to leave the disputed waters despite warnings by Japanese coastguard.
In June, the Japanese government expressed protest over Seoul holding its regular military exercise in the area of the disputed Liancourt Rocks.
In February, South Korean Foreign Ministry criticized Japan over holding a "Dokdo day" in the prefecture of Shimane and Tokyo's repeated claims to the disputed group of islands.
"The government of the Republic of Korea expresses strong protest over the fact that the Japanese government is repeating unjustifiable claims to Dokdo, as can be seen from the attendance of a high-level official of the central government at the provocative "Dokdo day" event hosted by the country’s provincial government on February 22, and urges that the event be discontinued for good," the ministry said in a statement.