Voters backed a motion put forward by conservative groups that Taiwan's Civil Code – which defines marriage as the union between a man and a woman – remain unchanged.
LGBT rights activists proposed two motions: legalisation of same-sex marriage under the Civil Code and compulsory gender equality education covering LGBT rights – both of which received less that 18 percent support.
Activists worldwide last year lauded Taiwan after its top court voted to legalise gay marriage, making it the first place in Asia to do so. The changes were due to be implemented within a year, but pressure from conservative campaigners has stalled progress.
The government said earlier said that the referendums would not stop it from bringing in the changes. A special law is expected to be passed, without amending the Civil Code.
Pro-independence party suffers
Saturday's votes came alonside local elections, which saw the ruling Democratic Progressive Party (DPP) dealt a massive blow in city and county seats.
President Tsai Ing-wen resigned as party leader, sparking questions over whether she will be able to run for re-election in 2020.
The pro-China former ruling party, Kuomintang (KMT) made gains, taking 15 of the 22 cities and counties up for grabs.
Tsai has promoted Taiwan as a beacon of democracy in the region since she took office, pitching it as a counterpoint to China's authoritarianism, as Beijing's influence on the island – which it considers its own territory – grows.
The nationalist KMT was once the main enemy of China’s Communist Party, with which it fought a decades-long civil war in the early 20th century.