The court unanimously upheld the claims of the applicants, the opposition Democrats (SDS), that holding the referendum on 4 May would disenfranchise voters since part of the early voting would be held during the May Day public holiday.
Setting 4 May as polling day would have "threatened the fairness of the referendum proceedings and consequently undermined legitimacy of the referendum decision."
The referendum decree was therefore found to be incompatible with Article 90 of the Constitution, which sets down referendum rules, and with Article 44, which gives every citizen the right to participate in the management of public affairs.
In handing down the verdict, it also rejected the argument of the National Assembly that the topic is too important to be mixed with the EU elections, which will be held on 25 May, the date sought as polling day by the referendum initiators.
One reason the SDS wanted the referendum to coincide with the EU election is the new rules on quorum, enacted in 2012 as amendments to the Constitution.
The Constitution stipulates that a law is rejected in a referendum if a majority of voters who have cast valid votes vote against the law, provided at least one fifth of all qualified voters have voted against.
While the Court did not rule on substance whether referenda and elections can be mixed, it said there were no grounds to reverse a decision from 1996 in which it ruled that holding elections and referendum on the same day does not run afoul of the Constitution.
It was not immediately clear whether the decision meant that the referendum can now be held on 25 May or at a later date.
The referendum revolves around the question of whether the latest changes to the archives law would open Yugoslav-era archives as the coalition claims, or close them as the opposition fears.