The result has been seen as a setback to LGBT couples who were hoping their island would be the first place in Asia to let same-sex couples share child custody and insurance benefits.

The vote on Saturday, organised by Christian groups that make up about five per cent of Taiwan's population and advocates of the traditional Chinese family structure, goes against a May 2017 Constitutional Court ruling.

Justices told legislators then to make same-sex marriage legal within two years, a first for Asia where religion and conservative governments normally keep the bans in place.

Although the ballot initiative is advisory only, it is expected to frustrate politicians who are mindful of public opinion as they face the court deadline next year.

Many legislators will stand for re-election in 2020.

"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.

Ruling party politicians backed by President Tsai Ing-wen had proposed legalising same-sex marriage in late 2016, but put their ideas aside to await the court hearing.

Opposition to same-sex marriage rose after the court ruling, as opponents held rallies and mobilised votes online.

Courts will still consider local marriage licensing offices in violation of the law by May 2019, if they refuse same-sex couples, a Ministry of Justice spokesperson said last week.

"The referendum is a general survey, it doesn't have very strong legal implications," said Shiau Hong-chi, professor of gender studies and communications management at Shih-Hsin University in Taiwan.

"One way or another it has to go back to the court."

Voters approved a separate measure on Saturday calling for a "different process" to protect same-sex unions.

Australian Associated Press