The trio, all former ministers in the regional government of ousted Catalan leader Carles Puigdemont, faced a European arrest warrant issued against them in March by Madrid.
Puigdemont and four of his ministers fled to Brussels in October last year to avoid facing charges including rebellion related to their push for secession from Spain.
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The court "has ruled that the three Spanish European Arrest Warrants are irregular and therefore refused their execution," said a statement from the Dutch-speaking Brussels Court of First Instance.
"The council chamber shares the view of the public prosecutor and the defence that there are no valid underlying national laws corresponding to the content of the European arrest warrants," it added.
Spain wants the ex-ministers -- Meritxell Serret, Antoni Comin, Lluis Puig -- to face charges of rebellion, misuse of public funds and disobeying the state for organising last year's referendum on Catalan independence, which Madrid deemed illegal.
Puigdemont was arrested in Germany on the Spanish warrant last month but a German court refused to extradite him on the rebellion charge. The court instead ordered his release on bail pending a hearing on a lesser charge.
The fourth Catalan politician who fled to Belgium with Puigdemont, Clara Ponsati, has since fled again to Scotland, where she too is facing extradition proceedings.