Puigdemont gave a televised address from Belgium at a campaign rally on Monday, telling the central government in Madrid that his party would win the election.
According to the statement released by the Spanish court, Llarena argued that the European warrant would complicate the overall probe into Catalan leaders.
Despite the withdrawal of the warrants today, the judge in Spain said the group still faced possible charges for sedition and rebellion, with the latter carrying up to 30 years in prison.
Photo The ousted Catalan leader Carles Puigdemont, third from left, at an event in Brussels with mayors and former councillors from the region this month.
Madrid called the new elections after the independence declaration, while dismissing Catalonia's government and suspending the region's autonomy.
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Judge Pablo Llarena, who is in charge of the case, also withdrew warrants for the arrest of four other Catalan politicians who fled Spain with Puigdemont: Antoni Comin, Lluis Puig, Meritxell Serret and Clara Ponsati.
But Marta Rovira, Junqueras's deputy in his ERC party, said the decision was politically motivated.
"Now there is no reason for Puigdemont not to return to Spain, not to put himself in front of the people he wanted to liberate, because he declared independence and went running off", Esteban Gonzalez Pons, a spokesman for the ruling Popular Party in the European Parliament, said.
Puigdemont, Junqueras and other former ministers are candidates for the elections, despite being in exile or prison.
Teneo Intelligence analyst Antonio Barroso said the decision to keep the four separatist leaders in jail "will certainly help the separatists to focus their messaging on the alleged repression by Spanish authorities, rather than on any prospective policy issues".
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However, pro-independence parties view the election as a proxy vote on a split from Spain.
Campaigning began on Tuesday, with polls predicting a close race between the pro and anti-independence camps. Polls show both sides neck and neck on a high turnout.
Spanish Prime Minister Mariano Rajoy and fellow opponents of Catalan independence, meanwhile, have hitched their hopes on a record turnout on December 21 to return a legislature in favour of unity with Spain.
The warrant was originally issued after Puigdemont and Antonio Comin, Lluis Puig, Meritxell Serret and Clara Ponsati travelled to Belgium in the wake of the Catalan unilateral declaration of independence on October 27.
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