A majority of Croatians have voted in a referendum to ban gay marriages in what is a major victory for the Catholic Church-backed conservatives in the European Union's newest nation.

The state electoral commission, citing initial results, said 65% of those who voted answered "yes" to the referendum question: "Do you agree that marriage is matrimony between a man and a woman?" About 34% voted against.

The result meant that Croatia's constitution will be amended to ban same-sex marriage.

The vote has deeply divided Croatia. Liberal groups have said the referendum's question infringes on basic human rights. The church-backed groups have gathered 750,000 signatures in its support.

The country of 4.4 million, which became EU's 28th member in July, has taken steps to improve gay rights, but issues such as same-sex marriage remain highly sensitive.

The referendum was called by conservative group In the Name of the Family after Croatia's centre-left government drafted a law to let gay couples register as "life partners".

The Catholic church's leaders have urged their followers to vote "yes" in the referendum. Nearly 90% of Croatians are Roman Catholics.

"Marriage is the only union enabling procreation," Croatian cardinal Josip Bozanic said in his message to followers. "This is the key difference between a marriage and other unions."

Several hundred gay rights supporters marched in the capital, Zagreb, on Saturday urging a "no" vote.

"I will vote against because I think that the referendum is not a festival of democracy, but a festival of oppression against a minority, which fights for its rights and which does not have its rights," Jura Matulic, a university student, said.

Croatia's liberal president Ivo Josipovic said he would vote against amending the constitution.

"We don't need this kind of a referendum," Josipovic said. "Defining marriage between a man and a woman doesn't belong to the constitution. A nation is judged by its attitude toward minorities."

Prime Minister Zoran Milanovic said that "this is the last referendum that gives a chance to the majority to strip a minority of its rights".

The EU hasn't officially commented on the referendum, but has clashed with Croatia over some of its other laws, including an extradition law that has prevented its citizens from being handed over to the bloc's other member states, which Croatia had to amend under pressure from Brussels.