The museum, which opened Thursday and is run by the Japanese government, displays documents and photographs defending Japan's claims over two sets of islands that China and South Korea also see as their own.
Japan has a longstanding 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.
China said today that the Diaoyu islands have been its "inherent territory since ancient times".
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"We are strongly dissatisfied with what the Japan has done, and I want to emphasise that nothing can change the fact that Diaoyu belongs to China," foreign ministry spokeswoman Hua Chunying told a regular press briefing.
"We remain resolute in safeguarding our sovereignty over the Diaoyu islands."
The criticism comes as Japanese Foreign Minister Taro Kono is set to visit Beijing this weekend for talks with Chinese counterpart Wang Yi on Sunday.
"We hope that through this visit the two sides can implement the important consensus reached by the two leaders, and promote improvement in the development of bilateral ties."
The two sides are also expected to discuss the North Korean nuclear issue.
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