This is despite the fact that a court ruling last year on same sex unions ordered for legislation to be made within the next two years to allow gay marriage as well.
Many LGBT couples were hoping their island would be the first place in Asia to let same-sex couples share child custody and insurance benefits.
There was a series of votes on Saturday, including local elections with caused the President of Taiwan to quit.
Several votes were proposed, each by different groups: one (Case 10) that marriage should stay defined in the civil code as being between a man and a woman (which received 7.6 million votes), one (Case 12) saying same-sex unions should be protected under a different law (6 million) and another (Case 14) asking if same-sex couples should have equal marriage rights (3 million).
Although the ballot initiative is advisory only and politicians face the court deadline next year.
"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.
Opposition to same-sex marriage rose after the court ruling in 2017, 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."
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