Delegates attending the World Health Assembly (WHA) in Geneva later this month were supposed to receive their invites by Monday.
Taiwan, which is fighting international marginalisation as Beijing puts pressure on its allies, said it had not received one.
"Mainland China pressured the WHO and blocked it from issuing us an invitation... we express strong dissatisfaction and protest," the island's Mainland Affairs Council said in a statement.
Relations with China have become increasingly frosty since Beijing-sceptic President Tsai Ing-wen took power almost a year ago.
China still sees self-ruled Taiwan as part of its territory awaiting reunification and is incensed that Tsai will not agree to the concept that there is only "one China", unlike her Beijing-friendly predecessor Ma Ying-jeou.
Under Ma, Taiwan was granted "observer status" at the WHA in 2009 -- a rare acknowledgement on the global stage.
But since Tsai took the helm, Beijing has sought to block the island from a string of international events.
China reiterated its demand that Taiwan must accept the "one China" principle and blamed Tsai's traditionally pro-independence Democratic Progressive Party (DPP) for the WHA snub.
"The DPP has damaged the joint political basis of cross-strait relations, so the precondition for Taiwan to attend no longer exists," China's Taiwan Affairs Office said in a statement Monday.
The island was expelled from the WHO in 1972, a year after losing the "China" seat at the United Nations to Beijing.
With China in the ascendant, Taiwan has shed global allies in recent decades, with only 21 countries now recognising the island's sovereignty.
Even its most powerful ally, the United States, has no official diplomatic relations.
US President Donald Trump recently rebuffed the idea of another phone call with Tsai after their protocol-busting chat following his election victory, saying he would not want to damage relations with China's President Xi Jinping.
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