Beijing frequently detains foreign nationals suspected of crimes for long periods before arresting them and putting them on trial.
The man, an employee of the Japanese pharmaceutical company Astellas, was held in March last year and placed under formal arrest in October.
In recent days, Japanese media outlets, citing diplomatic sources, reported that the man had been indicted for spying.
Asked about the case on Thursday, Beijing's foreign ministry confirmed China has "brought a public prosecution against the relevant Japanese national suspected of espionage."
"China is a country under the rule of law. We investigate illegal and criminal activity in accordance with the law while guaranteeing the legal rights and interests of the perpetrators," ministry spokesperson Mao Ning said at a regular briefing.
"It is hoped that the Japanese side will more strongly guide its citizens to abide by Chinese laws and regulations, and not take part in illegal and criminal activities in China," she added.
Mao declined to give specific details about the case, referring reporters instead to the "competent Chinese authorities".
Japan's embassy in Beijing did not respond to a request to comment on the case sent by AFP on Wednesday.
And a spokesman for Astellas Pharma told AFP: "it is true that he has been indicted. But beyond that, we would like to refrain from commenting as the lawsuit is ongoing."
The arrested man has reportedly worked in China for two decades and was previously a senior executive at a major Japanese business lobby in the country.
He was planning to return to his home country before his sudden detention, according to Japan's Kyodo News Agency.
Beijing has detained a series of people, both Japanese and Chinese, in recent years on allegations of spying for its island neighbour.
In October 2019, Chinese authorities detained a Japanese professor -- reportedly on suspicion of spying -- until he was released and returned to Japan the following month.
And in March 2020, China said it had arrested one of its own citizens reportedly working as a university professor in Japan, claiming he had confessed to spying.
Beijing and Tokyo have long butted heads over territorial disputes, Japan's colonial history and other flashpoints.
They flared again last month when Japan signed a key defence pact with the Philippines, with an apparent eye on curbing Beijing's sweeping claims to sovereignty in the East and South China Seas.
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