The authorities in Taiwan have accused Kenya of using guns and tear gas to force 37 Taiwanese on to a plane bound for mainland China.
Eight other Taiwanese were deported to mainland China on Monday, prompting Taiwan to accuse Beijing of "extrajudicial abduction".
China has praised Kenya for supporting its "one-China policy".
Beijing views Taiwan - self-ruling since 1950 - as a renegade region that must be reunited with the mainland.
It insists that other countries cannot recognise both China and Taiwan, with the result that Taiwan has formal diplomatic ties with only a few countries.
Taiwan does not have formal diplomatic relations with Kenya.
Taiwan's foreign ministry said Kenyan police had forced 22 Taiwanese citizens, arrested on suspicion of fraud, to board a plane bound for China on Tuesday, despite protests from John Chen, Taiwan's representative to South Africa.
Another 15 Taiwanese, who had been acquitted in the case, were also coerced into boarding the plane, it said.
Officials said some of the deportees had tried to prevent Kenyan police from entering their jail cell, as video posted by Taiwan's Central News Agency appears to show.
The police broke down a wall, "threw tear gas" and brandished "assault rifles" to force them on to the plane, Antonio CS Chen, the chief of the West Asian and African Affairs section of Taiwan's foreign ministry, told reporters.
He said Chinese diplomatic officials had been present.
Kenyan government spokesman Eric Kiraithe defended the legal process that had led to the deportations.
He said Kenyan courts relied on information available and he rejected what he called media insinuations.
An interior ministry spokesman told Reuters news agency the 37 people had come "from China and we took them to China", adding that Kenya had "an obligation to ensure if people are here illegally they are taken back to where they came from".
When asked about the case, Chinese foreign ministry spokesman Lu Kang told reporters: "The one-China policy is an important pre-condition for bilateral relations with China and other countries. We commend Kenya for its upholding of this policy."