In their Golden Horse coverage, Chinese media outlets quickly scrubbed clean any references to Fu and her winning documentary "Our Youth in Taiwan", a film about a 2014 student protest movement on the island.
Director Fu Yue said during her acceptance speech Saturday in Taipei that her biggest hope was for "our country" to be regarded as an "independent entity".
Mainland Chinese former Best Actor victor Tu Men then raised more eyebrows by saying he was honoured to present an award in "China, Taiwan" a phrase many Taiwanese object to.
However, he added: "We hope that art can be art, and that no political issues will interfere with it because art is very pure".
Taiwan split from mainland China amid civil war in 1949, but Beijing considers the self-ruled island part of its territory.
In an interview at the Presidential Office Building today, Tsai Ing-wen said sporting events continue to remain one of the best ways for Taiwan to break through diplomatic difficulties.
"Here [in Taiwan] there aren't people who will disappear or be silenced for expressing differing viewpoints", she wrote, "and we also don't have sensitive terms that are censored on the internet".
"I am proud of yesterday's Golden Horse Awards, that highlights the differences between Taiwan and mainland China, because of our freedom and diversity, and this is why this is a place where artistic creations can be free", she added in a Facebook post.
"Taiwan is a democratic and open society", she said.
The team's athletic prowess led them to win five gold, one silver, and a bronze medal in the competition hosted by South Africa.
Other Chinese celebrities like Hu Ge (胡歌) who was one of the presenters at the ceremony, best leading actress nominee Sun Li (孫儷), and her husband Deng Chao (鄧超), a best actor nominee, rushed to leave Taiwan Sunday morning, apparently reluctant to get involved in the political controversy.
The Facebook pages of Fu and Cheng have been inundated with critical comments, "which is a form of cyber bullying we are opposed to", Tsai said "Any individual who expresses his or her opinions freely should not be subject to bullying or psychological threats".
In a separate statement on Monday, Taiwan's ruling Democratic Progressive Party said the criticism of Fu was an attempt at "election interference from outside forces".
Minister of Culture Cheng Li-chiun (鄭麗君), in a Facebook post with photograph of her and Fu, said the Golden Horse Awards were an global award that respects the art of filmmaking and creative freedom. She was fined for tax evasion last month and in her apology said her achievements were inseparable from the Communist Party.
When Fu was speaking, the live broadcasting of the ceremony on China's online platforms was cut off, while Chinese actress Fan Bingbing (范冰冰), along with other Chinese artists, immediately posted comments on their Weibo accounts saying that "China allows for no loss of its territory, even a bit". Fan shared the post over the weekend that was first published by The Communist Youth League of China, saying "China can not miss out on any inch", together with a map of China that includes Taiwan and the South China Sea.