Taiwanese officials said the five were flown to China despite a Kenyan court order for them to return to Taiwan.
Chinese authorities said they were suspected of telecoms fraud which targeted people in mainland China, and should be tried in China.
Taiwan does not have formal diplomatic relations with Kenya.
On Friday the five, along with 35 Chinese nationals, were acquitted of allegedly running an unlicensed telecommunication system on the grounds that the prosecution had failed to prove their involvement, AFP news agency reports.
This is the latest incident in which Chinese authorities have managed to get Taiwanese fraud suspects deported to Beijing.
Taipei has also protested against deportations from Malaysia and Cambodia to China.
In April, Kenyan authorities handed over 45 other Taiwanese people, suspected of conducting telephone scams, to Beijing.
Taiwan labelled the incident “extrajudicial abduction”, saying they had been forced on board a plane by Kenyan police wielding rifles and tear gas.
At the time, Chinese authorities praised Kenya for supporting its “one-China policy”.
Beijing views Taiwan – self-ruling since 1950 – as a breakaway 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.