Taiwan in May unsuccessfully bid for full membership of the WHO, after years of being refused even observer status.
Taiwanese authorities cited a case this July of two tuberculosis patients travelling by air from Taiwan to Nanjing in China via Hong Kong, one of whom was multidrug-resistant.
The Taiwanese Centres for Disease Control (CDC) "promptly reported the case to the WHO" and notified Chinese authorities, but received no response, according to a statement distributed by the island's representation bureau in Geneva.
In the absence of any response, Taiwan sent experts to China to make special arrangements for the patients' return, including chartering a small boat and using a medical helicopter, it said.
However, "for the passengers and cabin crew in the same flight with this couple on their way from Taiwan to Hong Kong, 285 of them including citizens from the United States, Indian, Japan and the Netherlands, each needs to be alerted and advised," the statement said.
"The gap caused by Taiwan's exclusion from the IHR (International Health Regulations) not only threatens Taiwan's health security, but also puts other countries at great risk," it warned.
It noted that some 1.3 million migratory birds fly over Taiwan annually. Migratory birds are seen as a key factor in the spread of avian flu.
Taiwan was evicted from the agency in 1972, a year after losing the "China" seat in the United Nations to Beijing.
The current head of the WHO, Margaret Chan, is a Chinese national.
China has considered Taiwan a part of its territory since Nationalist armies fled the mainland at the end of a civil war in 1949, and has vowed to retake the island by force if it declares formal independence.