The judge is expected to rule on the warrant Friday, but the process could be complicated if Puigdemont decides to seek asylum in Belgium.
Spanish prosecutors have asked the National Court to jail nine ex-members of the sacked Catalan government.
"We have to admit that because this is a very special case it could pose political questions", said Maxime Chome, a lawyer and legal expert at Brussels Free University.
Mr Puigdemont's lawyer in Belgium said his client would stay away from Spain while the political climate was "not good"; but he would cooperate with the courts.
Spain has been gripped by a constitutional crisis since the referendum was held on 1 October in defiance of a constitutional court ruling that had declared it illegal.
The detention of the secessionist leaders and Puigdemont's flight to Belgium make it hard for leading figures from the independence movement to stand in a snap election in the wealthy region called by the Spanish government for December 21.
Former Trump campaign adviser denies encouraging aide on Russian Federation dealings
After the news of the indictments broke, The Washington Post and CNN reported that Trump was seething in the White House about the news.
Former ministers in the deposed Catalan government arrive at court.
According to Spain's chief prosecutor, the Catalan leaders were accused of rebellion - which carries a maximum 30-year jail term - as well as sedition and misuse of funds.
Puigdemont and four others fled to Belguim after the three day ultimatum to pay a deposit of €6.2m ($7.2m) to cover potential liabilities which was stated in the court summons, expired.
The prosecutor's request came after the nine ex-ministers were quizzed at the National Court on possible charges of rebellion, sedition and embezzlement.
Five senior regional lawmakers and the speaker of the Catalan parliament, Carme Forcadell, were summoned by the Supreme Court, which handles the cases of people who enjoy parliamentary immunity.
The Supreme Court said the hearing of the six regional parliament board members was postponed until November 9 following a request by their lawyers.
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