"Relevant Chinese authorities took criminal coercive measures this month against a Japanese citizen, in accordance with the law," foreign ministry spokesperson Mao Ning told a regular press briefing.
"This Japanese citizen is suspected of engaging in espionage activities, in violation of the criminal law and the anti-espionage law of the People's Republic of China," Mao said.
"China is a country under the rule of law. All foreign nationals in China must abide by Chinese laws, and offenders are prosecuted according to law," she added.
Japanese government spokesman Hirokazu Matsuno told reporters earlier on Monday that Tokyo's embassy in China had been informed "this month that a Japanese man in his fifties was detained in Beijing."
He gave no details on the man's identity, his alleged crime, or when he had been arrested.
"Ever since we learned about this case, the Japanese government has been strongly urging the immediate release of this Japanese national," Matsuno said.
He added that Tokyo was also seeking consular access to the man, who has not been named publicly.
The man is an employee of the Japanese pharmaceutical firm Astellas, a spokesman for the company told AFP, declining to offer any further details.
The company was working with Tokyo's foreign ministry to gather more information and take appropriate action, he added.
Local media described the man as a veteran expat in China who had worked in the country for two decades.
Kyodo News Agency reported he was detained just before his planned return to Japan this month, and that he had previously been "a senior executive of the Japanese Chamber of Commerce and Industry in China."
Beijing on Monday said "similar cases have occurred repeatedly among Japanese citizens in recent years."
"Japan should better educate and warn its citizens," Mao said.
In October 2019, Chinese authorities detained a Japanese professor, reportedly on suspicion of spying.
He was released and returned to Japan the following month.
And in March 2020, China's foreign ministry said it had arrested a Chinese man reportedly working as a university professor in Japan who they claimed had confessed to spying.