"Excluding Taiwan from WHO not only jeopardises the right to health of the 23.5 million people of Taiwan, it also seriously undermines WHO's efforts to achieve health for all," Hsueh Jui-yuan told an event hosted by the Geneva Press Club.
He spoke shortly before the World Health Organization's annual assembly kicked off in Geneva on Sunday.
Taiwan has been blocked from attending the World Health Assembly (WHA) in recent years by China, which considers the island a renegade province to be reunified with the mainland.
There have been growing calls to allow Taiwan in as an observer, especially after the Covid-19 pandemic highlighted the importance of global cooperation on reining in infectious diseases.
Hsueh warned that leaving Taiwan out in the cold hampered the swift and efficient sharing of information that would be needed to prevent or more efficiently respond to the next pandemic threat.
"I am afraid that Taiwan will become the gap of the next pandemic," he said, speaking through a translator, warning that would "have a terrible impact for the entire world."
Washington has warned of the negative consequences of continuing to exclude Taiwan.
"As we continue to confront emerging health threats around the world Taiwan's isolation from WHA76... undermines inclusive global public health cooperation led by WHO," the US mission in Geneva tweeted Saturday.
Beijing has staunchly opposed efforts to include Taiwan as a WHA observer. "Any attempt to play the 'Taiwan card' to contain China will lead nowhere," the Chinese foreign ministry said recently.
Taiwan was expelled from the WHO in 1972, a year after losing the "China" seat at the United Nations to the People's Republic of China.
It was allowed to attend the WHO's top annual meetings between 2009 and 2016 as an observer when relations with China were warmer.
But Beijing has stepped up its campaign to pressure Taipei since President Tsai Ing-wen came to power, as she refuses to acknowledge its stance that self-ruled democratic Taiwan is part of China.
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