Matsuno said Tokyo had received no prior request from Seoul for such research.
“We strongly demand this immediate shutdown,” he said.
He said the two sides had held talks over the incident but both reiterated their previous claims to the territory.
In Seoul, South Korea’s foreign ministry said it could not accept the Japanese complaint. He called the investigation a legitimate act carried out in accordance with national and international law.
In 2017, Japan filed a lawsuit against South Korea after the official website of the Pyeongchang Olympics branded the islands as Dokdo.
Japan and South Korea enjoy rich cultural ties, but relations have been marred by bitter tensions over historical issues such as Japan’s colonization of the Korean peninsula in the last century and its actions during World War II.
Japan also has a dispute over Japanese-controlled islands in the East China Sea which it calls Senkaku, which China claims and also calls Diaoyu.
Associated Press writer Hyung-jin Kim in Seoul, South Korea, contributed to this report.
Yuri Kageyama is on Twitter https://twitter.com/yurikageyama
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