Taiwan has no diplomatic ties with Kenya, which recognises the government in Beijing.
Taiwan said Tuesday 37 of its citizens in custody in Kenya were set to be deported to China, a day after accusing Beijing of "abducting" a group of eight Taiwanese from the east African nation.
Fifteen of the group had been cleared of involvement in a telecoms scam by a Kenyan court, the foreign ministry said.
The remaining 22, who were believed to be currently aboard a Chinese plane awaiting departure, had not faced trial following their arrest Friday on similar charges, it said.
Taiwan has no diplomatic ties with Kenya, which recognises the government in Beijing. Its nearest diplomat is based in the South African capital.
"Early this morning... we were notified that the mainland and Kenya may be attempting to send (the suspects) to China," said Chen Chun-shen, chief of West Asian and African affairs at Taiwan's foreign ministry.
"Our colleague went immediately to the prison to see the detainees but faced all kinds of impediment," Chen told reporters in Taipei.
He added that three people from China's Kenyan embassy were also present.
Of the eight Taiwanese already sent to Beijing, one of them has an American passport, Taiwan's foreign ministry said.
Mainland authorities did not have any immediate comment on the new developments and Taipei was also seeking a response.
Asked to comment on the row Monday, China's foreign ministry said it needed to check on the details but "the One China policy should be upheld".
China still regards Taiwan as part of its territory awaiting reunification, by force if necessary, even though Taiwan has ruled itself since 1949.
The mainland is stepping up pressure on Taiwan's president-elect Tsai Ing-wen — who is set to take office in May — as Beijing does not trust her historically pro-independence party.