After receiving a request to free the 10 Catalan leaders, Supreme Court Judge Pablo Llarena decided there was a risk that Junqueras and three others would repeat their alleged offences if released.
But Puigdemont's Belgian lawyer, Paul Bekaert, said that the Catalan separatist leader wasn't planning an immediate return.
The explanation Llarena gave for his decision was that the crime of "rebellion", which carries a possible prison sentence of 30 years, does not exist in Belgium, meaning that if Puigdemont was returned to Spain by the Belgian authorities, it would be to face the lesser charge of misuse of public funds and the Spanish court would not be able to try him for the more serious offense.
For those who understand European Arrest Warrant system, the move was inevitable.
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Puigdemont fled to Belgium after declaring his region independent from Spain in a referendum that saw voters in Catalonia vote overwhelmingly to secede from Madrid's control - although the ballot was not sanctioned by Madrid and less than half of the electorate turned out to vote.
Last month, Spain's central government issued the warrants for Puigdemont and four of his allies-Meritxell Serret, former agriculture minister; Antoni Comín, former health minister; Lluís Puig, former culture minister; and Clara Ponsatí, former education minister.
Official campaigning for a 21 December regional election, which was called after Puigdemont's government was dissolved, started on Tuesday.
The Associated Press reports that the five are facing charges of sedition, rebellion and embezzlement related to their roles in staging an independence referendum in October that Spain declared illegal.
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Mr Puigdemont, who is standing for re-election to the regional parliament, would nearly certainly face arrest on his return, as the charges of rebellion and sedition against him have not been lifted.
Catalan separatist parties that tried to break away from Spain would lose their absolute majority in regional parliament in elections later this month, an influential opinion poll showed Monday.
The Spanish government has said the early election is an attempt to find a democratic way out of the nation's worst crisis in almost four decades. Puigdemont would be arrested if he went to Spain, he said. Puigdement is running as the candidate for the Junts Per Catalunya party, despite his exile. He said it remained to be seen whether his pledge to abide by Spanish law was "truthful and real".
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