Chinese artists in recent years have largely stayed away from Taiwan's Golden Melody Awards given renewed tension between democratically governed Taiwan and China, which views the island as its territory.
The reference to Tiananmen is unlikely to endear Beijing to the ceremony.
Taking the stage on Saturday after winning for best Taiwanese language album at the ceremony in Taipei, Panai noted it was the 35th anniversary of the awards.
China has quashed major commemorations of the 35th anniversary of the Tiananmen Square crackdown. (AP PHOTO)
"The Tiananmen Square incident is also exactly 35 years old, let's not forget," she said.
Chinese tanks rolled into the square before dawn on June 4, 1989, crushing weeks of pro-democracy demonstrations by students and workers.
China has never provided a full death toll, but rights groups and witnesses say the figure could run into the thousands.
Public discussion of what happened is taboo in China, although it is freely discussed in Taiwan.
China says it "long ago" reached a clear conclusion about the events of 1989.
China's Taiwan Affairs Office did not immediately respond to a request for comment.
Panai has campaigned for years for the rights of Taiwan's indigenous people.
"Democracy is a lengthy and not an easy journey," she told reporters backstage after her win.
"We are pressured as we don't know if we will be bullied by a bigger power.
"The reason why I mentioned that event on stage is because Taiwan's democracy is a process that all of us need to cherish; our freedom and freedom of speech is what we need to protect."
Taiwan President Lai Ching-te, quoting Panai's Tiananmen comments on his Facebook page, praised the freedom artists have in Taiwan.
"Music is life, and music is also unfettered freedom," he said.
"We will continue to protect and defend the freedom of all musicians to create."
No Chinese singers attended this year's awards, despite several high-profile nominations including Xu Jun winning for best composer.
Another Chinese singer, Jude Chiu, did arrive in Taiwan but returned to the country before the awards for health reasons, Taiwan's official Central News Agency reported.
While Taiwan has only 23 million people, its pop music scene has an outsized cultural influence across East Asia, especially in China, partly due to creativity unencumbered by censorship.
The awards celebrate Mandopop and artists singing in Taiwanese, also known as Hokkien, Hakka and indigenous languages such as Bunun - a sign of the Taiwan government's efforts to promote once-suppressed tongues.
