Yuan Keqin was investigated on suspicion of espionage and had "confessed to the facts of the crime", ministry spokesman Geng Shuang said at a regular press briefing.
He was responding to a question from Japanese media about a professor at the Hokkaido University of Education who disappeared after travelling to China last June.
Yuan had returned for a family funeral and had been out of contact since, Japanese news agency Kyodo reported in December.
Geng did not confirm any details about Yuan's background but said there was "unambiguous evidence" of his guilt, adding that his case had been transferred to authorities for review and prosecution.
A group of Japanese researchers have issued an emergency appeal for the scholar, who specialises in East Asian political history, according to Kyodo.
A Japanese man detained by Beijing -- reportedly also on suspicion of espionage -- was released and returned to the country, government officials in Tokyo said last November.
Japanese media identified him as a professor from Hokkaido University.
Beijing said the man, identified as Nobu Iwatani, had confessed to collecting classified information from China.
China also detained six Japanese citizens for alleged "illegal activities" in 2017.
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