Lee Meng-chu was believed to have arrived in Hong Kong on August 18, and had then crossed the border into Shenzhen on August 20.
Family and friends said they had not heard of him since August 20, and concerns were raised that he might have been detained for his support of Hong Kong’s ongoing anti-government protests.
Ma Xiaoguang, a spokesman for the Taiwan Affairs Office, said at a regular media briefing in Beijing on Wednesday that Lee is under investigation.
Late last month, Taipei called on the mainland authorities to provide information on the missing man’s whereabouts.
Lee is an adviser to a township in Taiwan’s Pingtung county and an official there had said that Lee had posted comments supporting Hong Kong protesters on his Facebook page.