The 66 government officials will hold talks in Slovakia on Friday before travelling to the Czech Republic and Lithuania to boost trade ties and investment.
All three countries gave coronavirus vaccines to Taiwan, which has accused Beijing of hampering its efforts to secure enough doses.
The European Union members have shown signs of wanting closer relations with the island, even if that angers China.
Czech-Taiwanese Chamber of Commerce head Pavel Divis said in a statement the visit was "a unique opportunity for us to establish cooperation in sectors in which Taiwan is a global leader".
But the visit angered China.
"Taiwan is an inalienable part of China's territory, and the government of the People's Republic of China is the sole legal government representing China," Chinese foreign ministry spokesman Wang Wenbin said.
The visit also comes after President Joe Biden told a CNN town hall the United States would defend Taiwan if the island was attacked by China, a statement at odds with the long-held US policy known as "strategic ambiguity."
The Taiwan delegation will comprise Kung Ming-hsin, the national development council minister, and Wu Tsung-tsong, science and technology minister.
Taiwan Foreign Minister Joseph Wu is due to visit Prague on October 27.
Only 15 countries officially recognise Taipei rather than Beijing, which says the self-ruled democratic island as part of its territory and has vowed to one day re-take it -- by force if needed.
Beijing insists on a one-China policy that means countries cannot also give diplomatic recognition to Taiwan.
Wenbin added China "deplored and firmly opposed" such visits, threatening "universal condemnation" to countries receiving the delegation.
"We would also admonish the Taiwan authorities that any attempt to solicit foreign support and seek political manipulation is doomed to fail," he said.
Prague drew China's ire last year when a delegation of about 90 Czech politicians, entrepreneurs, scientists and journalists led by senate speaker Milos Vystrcil visited Taiwan for five days.
Lithuania in turn set up Taiwan's representative office in Vilnius under the name "Taiwan" instead of "Taipei", a move seen as a significant diplomatic departure from standard practice.
Beijing withdrew its ambassador to Lithuania and demanded Vilnius do the same, which it eventually did.
Slovakia is also considering sending a delegation to Taiwan. The plan is due to be discussed during the upcoming visit.
On Thursday, the European Parliament urged closer ties between the EU and Taiwan, calling for increased investment and slamming China over its treatment of the island.
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