The museum, run by the Japanese government, displays documents and photographs defending Japan’s claims over the islands.
Japan has a long-standing dispute with China over uninhabited islands in the East China Sea. They are administered by Japan, where they are known as “Senkaku”, but also claimed by China, which calls them “Diaoyu.”
Tokyo also claims islands in the Sea of Japan that are controlled by South Korea. They are known as “Dokdo” in Korean and “Takeshima” in Japanese.
“We hope this will be a key facility that deepens understanding on the Takeshima and Senkaku islands,” said Tetsuma Esaki, minister in charge of territorial issues, as he opened the museum, according to local media.
But Seoul reacted promptly, with the foreign ministry lodging an immediate protest over what it described as Japan’s “unjustifiable claims” to its “inherent territory”.
“We demand its immediate closure,” the foreign ministry said in a statement.
“The Japanese government should stop immediately its hopeless attempt to claim Dokdo, which is historically, geographically, and under international laws a part of our territory,” the ministry added.
The museum’s opening is also likely to anger China and comes after Japan recently spotted a Chinese nuclear-powered submarine prowling in waters surrounding the Tokyo-administered isles.
The Japanese government has long complained about China’s routine dispatch of coast guard ships to Japan’s territorial waters surrounding the islands.
Relations between Japan and China deteriorated in 2012 when Tokyo “nationalized” some of the islets.
Since then, the two countries have taken gradual steps to mend fences, but relations remain tense.