The foreign ministry gave the confirmation in a statement quoted by China's Global Times newspaper late yesterday, but did not specifically state that he had been detained.
The claim of endangering security is often used in cases of suspected espionage. The ministry said the Japanese embassy had been informed of the case.
There have been multiple reports in the Japanese press since mid-July about the man's disappearance. The Nikkei Business Daily identified him as the head of an organisation working to improve ties between the two nations.
The Japanese government's top spokesman Yoshihide Suga denied his country was involved in spying "against any nation", Kyodo added.
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Chinese authorities earlier this year arrested four Japanese on suspicion of spying.
The two countries have been taking steps for more than a year to improve relations that remain plagued by tensions over the legacy of World War II as well as a maritime dispute.