Beijing has confirmed it is investigating a Japanese suspected of "endangering China's national security", following Japanese reports that he had been detained, the latest irritant in relations between the two nations.

The foreign ministry gave the confirmation in a statement quoted by China's Global Times newspaper late Saturday, 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.

He was due to spend four days in Beijing for work but did not return home and has not been answering his mobile phone, Japan's Kyodo news agency said Saturday, quoting Japanese government and other sources.

The Japanese government's top spokesman Yoshihide Suga denied his country was involved in spying "against any nation", Kyodo added.

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.

Ties, however, remain shaky and Chinese allegations of espionage by Japanese have become a new source of friction.