By Agence France-Presse
Lee Ming-che, a 42-year-old NGO worker, had been unreachable since March 19 after he entered the southeastern Chinese city of Zhuhai from Macau, according to Taiwan's government.
On Friday China's official state news agency Xinhua reported that he was in detention and had "confessed" following interrogation.
Lee had "colluded with mainlanders...established illegal organisations, and plotted out and carried out activities to subvert state power," Xinhua cited a spokesman for the State Council Taiwan Affairs Office as saying.
"After interrogation, Lee and his group confessed to engaging in activities endangering national security," the spokesman was quoted as saying.
Lee, who works at a community college in Taipei, has long supported civil society organisations and activists in China.
"The Chinese authorities did not disclose any evidence related to the case at all," Taiwan's Mainland Affairs Council said in a late Friday statement reacting to the Xinhua report.
"Their vague and superficial responses cannot convince the people of Taiwan and also cannot convince the international community watching this case," it said.
Lee had been sharing "Taiwan's democratic experiences" with his Chinese friends online for many years and often mailed books to them, according to the Taiwan Association for Human Rights.
His detention is the latest in a series of incidents that have heightened tensions between Beijing and Taipei since China-sceptic President Tsai Ing-wen won Taiwan's elections last year.
Beijing mistrusts her independence-leaning Democratic Progressive Party, and has severed official communications with Taipei since she took office.
"It's alarming that sharing views and Taiwan's experience of democracy would be considered 'subversion'. Again, it shows the arbitrary use of the charge against free speech," Amnesty International China researcher Patrick Poon told AFP.
"If the Chinese authorities don't follow the cross-straits agreements on handling criminal suspects, it just shows that there is zero protection for Taiwanese citizens on the mainland," he said.
Last month, Beijing blocked Lee's wife from travelling to the mainland, with the airline telling her she could not board the plane because her travel permit had been revoked.
China's foreign ministry has not responded to request for comment from AFP.
Taiwan has been self-ruled since 1949 following a civil war on the mainland. But Beijing still claims it as part of its territory awaiting reunification, by force if necessary.