With the conservative vote passing the threshold of 25 percent of eligible electors, under referendum law the government must take steps to reflect the result. The move seemingly set Taiwan on the path to becoming the first country in Asia to legalize marriage equality. However, Taiwanese voters also ended up approving a referendum against the teaching of same-sex education in primary and middle school classrooms.
The office's Taiwanese counterpart fired back swiftly, saying the elections - along with referendums on topics such as same-sex marriage and Taiwan's name used at the Olympics - were an "internal affair whose results testified to the mature development of Taiwan's democracy".
Taiwan's President Tsai Ing-wen resigned as leader of the ruling Democratic Progressive Party (DPP) on Saturday after it suffered major defeats in key mid-term polls, a significant blow to her prospects for re-election in 2020.
While a referendum can not overturn a court ruling, it likely means that marriage equality will not be achieved in Taiwan through amendments to the Civil Code, but rather legislation will be passed to safeguard the rights of gay couples to enter same-sex unions.
"Having a special marriage law (for gay couples) means we are like second class citizens", he told AFP, adding that having a two-tier system would dent Taiwan's reputation as a trailblazer for equal marriage rights on the worldwide stage.
Underscoring Tsai's challenge are a series of public votes also held on Saturday on whether to make same-sex marriage legal, an issue which has deeply divided Taiwan.
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Gay rights activists had proposed that the Civil Code should give same-sex couples equal marriage rights, but only garnered three million votes.
"The legislature has lots of choices on how to make this court order take effect", said referendum proponent Chen Ke, a Catholic pastor in Taiwan and an opponent of same-sex marriage.
CNN quoted Central News Agency (CNA), a state-owned news agency operated by the Government of the Republic of China (Taiwan), reporting that Tsai apologised to the supporters of the party for the "disappointing performance" in a speech at its headquarters. "Rather, the outcome marked voters' dissatisfaction with President Tsai Ing-wen's governance".
The vote was just another headache in a bad result for Tsai, who has been attacked from both sides for her formerly strong positions on the issue.
"We will ... send our drafted bill to the parliament as soon as possible for review and passage because we respect same-sex partnerships and believe there should be a special law for them", he said.
Taiwan hosts the region's largest annual gay pride parade showcasing its lesbian, gay, bisexual and transgender (LGBT) community.
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But voters threw the Nationalists out of local offices in 2014 and the presidency in 2016 as they feared Ma had gotten too cozy with Beijing.
Taiwan's relations with China have deteriorated since Tsai came to power in 2016.
The party has indicated that it wants to strive for a better relationship with China.
Voters line up at a ballot station to vote for the city mayor in Kaohsiung, Taiwan, Saturday, November 24, 2018.
Taiwan's Investigation Bureau is probing Chinese influence on the elections through campaign funding of candidates.
As in previous elections it also tried to fuel fears about China.
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The Beijing-friendly main opposition Kuomintang (KMT) made gains in the face of China's increasing pressure on the island, which it sees as part of its territory to be reunified.