Spokesman for the Taiwan Affairs Office Ma Xiaoguang said Lee Ming-che, 42, was in good health, but gave no information about where he was being held or other terms of his detention.
Lee disappeared after clearing immigration on March 19 in the semi-autonomous Chinese territory of Macau and never showed up for a planned meeting later that day with a friend across the border in China.
"Regarding Lee Ming-che's case, because he is suspected of pursing activities harmful to national security, the investigation into him is being handled in line with legal procedures," Ma told reporters at a news briefing.
Cheng Hsiu-chuan, president of Taipei's Wenshan Community College where Lee has worked for the past year as a programme director, said Lee used WeChat to "teach" an unknown number of people about China-Taiwan relations under the government of Taiwan President Tsai Ing-wen.
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"For China, the material he was teaching would be seen as sensitive," Cheng said. WeChat has hundreds of millions of active users and is hugely popular as a means of communication in China.
However, in mid-2016 Chinese authorities shut down Lee's WeChat account and confiscated a box of books published in Taiwan on political and cultural issues, Cheng said.
"According to the news we've gotten, the state security bureau there doesn't know how to handle Lee's case," Cheng said.
On his most recent trip, Lee planned to see friends and obtain Chinese medicine for his mother-in-law in Taiwan, his wife, Lee Ching-yu said. He was expected to stay in the southern Chinese hub city Guangzhou through March 26, she said.
"I want the government of China to act like a civilized country and tell me what they're doing with my husband on what legal grounds and, like a civilised country, what they plan to do with him," Lee said.
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