A Japanese citizen "has been investigated on suspicion of endangering China's state security", the Foreign Ministry told China Daily on Sunday.
The ministry's spokespersons office did not reveal the identity of the man.
It said the investigation was conducted by "relevant departments" and the Japanese Embassy in China was notified.
Leading Japanese media reported on Thursday that the Japanese chief cabinet secretary Yoshihisa Suga confirmed that a suspect was detained.
Some Japanese media speculated that the man was detained for suspected espionage. But Suga, Tokyo's top spokesman, denied the alleged espionage at a news conference in Tokyo by claiming that "it is impossible that such actions will be taken against any country", according to Japan's Fuji Television.
Tokyo-based Jiji News Agency quoted unnamed sources saying that the man, aged more than 50 years old, was scheduled to visit China from July 11 to 15.
Japan News Network, a Chinese language website reporting Japan's news, quoted unnamed sources saying that the man is with Japan-China Youth Association.
The association the man is part of works on "developing Japan-China friendly relationship", according to the association's website.
However, the website is currently not accessible and it says "under maintenance".