Taiwan is excluded from most international organisations because of objections by China, which considers the democratically governed island its territory.
Taiwan attended the WHO's World Health Assembly (WHA) as an observer from 2009 to 2016 under the administration of then-President Ma Ying-jeou, who signed landmark trade and tourism agreements with China.
But Beijing began blocking Taiwan's participation in 2017, after President Tsai Ing-wen won office, for her refusal to agree to China's position that both China and Taiwan are part of "one China".
Chen Xu, China's permanent representative to the U.N. in Geneva, said there was no political basis for Taiwan to participate in the WHA, and accused Taiwanese officials of deliberately politicizing the issue of health.
"The so-called gap in the global epidemic prevention system is pure nonsense," he said, referring to calls by Taiwan and its allies for it to be included to better prevent pandemics.
Ahead of the decision, Taiwanese Health Minister Chiu Tai-yuan's said Taiwan's absence from the assembly was hindering pandemic prevention efforts.
"Taiwan's participation in the WHA and WHO is a matter of health, not politics," he said.