Also known by its French name Reporters Sans Frontieres (RSF), the Paris-based organisation decided against their original choice of Hong Kong, citing deteriorating freedom in the semi-autonomous Chinese city.
Taiwan is the freest in Asia at 51st place, according to RSF's 2016 World Press Freedom Index, while Hong Kong ranks 69th and China 176th.
Chinese dissident Wu'er Kaixi, who sits on RSF's emeritus board, said Hong Kong presented "real obstacles" for the watchdog to carry out its monitoring work.
He proposed the island as an alternative, citing its boisterous and competitive media landscape.
"Freedom of speech and freedom of press is absolutely not an issue in Taiwan. What might be a problem is the threat from China", Wu'er told AFP.
"RSF realised that China is the biggest threat to press freedom, so it decided to shift its focus to Asia," he added.
Taiwan's Beijing-sceptic President Tsai Ing-wen welcomed the organisation to Taipei.
The office in Taipei will also cover other East Asian countries including Japan, North Korea, South Korea, and Mongolia.
The opening "aims to better address the new challenges of media freedoms in this increasingly influential region of the world," RSF secretary general Christophe Deloire said in a statement released late yesterday.
Recent incidents in Hong Kong - including the disappearance of five publishers who were known for salacious titles about the Chinese leadership - have sparked fears that Beijing is choking the city's freedoms.
Taiwan is self-ruled but China regards the island as part of its own territory awaiting reunification under Beijing's rule. The two sides split following a civil war in 1949.
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