Beijing hit back at the criticism, saying the island had "no right" to be invited.
Self-ruling Taiwan is routinely prevented from attending global forums by Beijing, which still sees it as part of its territory requiring reunification.
But the island had been hoping to attend the triennial meeting of the UN aviation agency in Montreal later this month, after it was admitted in 2013 in a major breakthrough.
That invite came under previous Beijing-friendly president Ma Ying-jeou.
More From This Section
Taiwan's Mainland Affairs Council (MAC), which handles relations with Beijing, said Friday the island had not been admitted to the International Civil Aviation Organization (ICAO) meeting "due to political interference from China".
"(It) is a great loss for international aviation safety and the public's right to welfare protection," the MAC said in a statement.
Beijing said the move reflected the fact that Taiwan was not a sovereign state.
"The ICAO is a special agency of the UN, and only sovereign countries can take part in it," Chinese foreign ministry spokesman Lu Kang said at a regular briefing Friday.
Lu said that past arrangements had been made thanks to a "consensus" between Beijing and Taipei, referring to former president Ma's willingness to concede that there was only "one China", with each side allowed its own interpretation.
Tsai has never backed that concept, angering Beijing.
"For Taiwan's participation in any international organisation, the prerequisite is the 'one China' principle," Lu said.
Taiwan was a founding member of the ICAO but was thrown out in 1971 when it lost its UN seat to China.
The agency appointed China's Fang Liu as secretary-general last year.
"The government expresses strong regret and dissatisfaction," Foreign Minister David Lee told reporters.
Beijing has cut off all official communication with Taiwan since the new government took office.