The initiative wants the Constitution to define marriage as a heterosexual union.
In its warning, the Constitutional Court said that a decision confirming that the referendum was carried out in accordance with the Constitution meant that the Constitution was changed on referendum day.
The warning was issued after the agenda of the current parliamentary session was amended with a proposal to hold the marriage referendum on December 1.
The opposition and external members of the committee on the Constitution objected to the text of decision which proposed calling the referendum because they believe that if there was a vote in parliament after the referendum, parliament could turn down the will of the people.
The Constitutional Court said that in a people's referendum, called at the initiative of a people's initiative, voters decide on the referendum question, meaning that the people directly decide on changing the Constitution as proposed, in the form of the referendum question, by at least ten per cent of the electorate, by voting for or against the proposal.
The Constitutional Court said the marriage referendum would be the first time that the people directly decided on a concrete proposal to change the Constitution as proposed by voters.
Therefore, it is especially important that the decision and the procedure it would launch be in accordance with the Constitution because they would set a precedent not only for future parliamentary and referendum practice, but also for the true realisation of direct democracy in Croatia, the court added.