Relations with China have become increasingly frosty since Taiwan's Beijing-sceptic President Tsai Ing-wen took power.
Self-governing Taiwan, which China sees as a renegade province awaiting reunification, has been invited to attend the WHO's main annual meeting as an observer every year since 2009, but this year it did not receive an invitation.
Relations with China have become increasingly frosty since Taiwan's Beijing-sceptic President Tsai Ing-wen took power almost a year ago and China has sought to block the island from a string of international events.
In an interview with AFP Sunday, Taiwanese Health Minister Chen Shih-chung said he was "very, very disappointed" to be excluded from the meeting.
Representatives from 11 of WHO's 194 member countries, including Nicaragua, Paraguay and Belize, put forth a proposal on Monday -- the first day of the assembly -- to put offering Taiwan permanent observer status onto the agenda.
But the assembly decided without a vote to reject the proposal, leaving the issue off the agenda. Pro-Taiwan protesters were demonstrating in front of the UN as the gathering was under way.
Robert Browne, the health minister of St Vincent and the Grenadines which was among the countries behind the proposal, warned that "the exclusion of Taiwan erodes the credibility, integrity and effectiveness of this important assembly."
His counterpart from Palau, Gregorio Ngirmang, agreed, asking the assembly how he could be permitted to represent the 17,000 citizens of Palau at the meeting "while we ignore the 23 million people in Taiwan."
But China hailed the decision to leave Taiwanese observer status off the agenda, insisting that was Beijing's decision alone.
"Taiwan is part of China. Questions regarding Taiwan are China's internal affairs," the Chinese representative at the meeting said.
Under Tsai's Beijing-friendly predecessor Ma Ying-jeou, a cross-strait agreement was reached allowing Taiwan to sit in on the World Health Assembly as an observer.
Today "the political foundation for Taiwan China to participate in the assembly this year is not there anymore," the Chinese representative said Monday.
He rejected the notion put forth by the 11 countries that blocking Taiwan could hamper international cooperation and the rapid exchange of information on health matters.
The proposal's real agenda, he said, was to help Taiwanese "authorities to manipulate health issues in an attempt to expand their so-called international space and challenge the One china principle."