Puigdemont, who considers himself the rightful leader of Catalonia, is currently in Belgium. He has said he's not fleeing the Spanish court system but instead is seeking European support for his region's independence bid.
Puigdemont tweeted Saturday that he and his associates are "prepared to fully cooperate with Belgian justice following the European arrest warrant issued by Spain."
Spain was plunged into its worst political crisis in decades after Puigdemont's administration held an independence referendum October 1 despite the nation's highest court banning the move.
The Catalan parliament then declared unilateral independence, and Madrid responded by suspending the region's autonomy, sacking the government and imposing direct rule.
Carmen Lamela, a judge in Spain's National Court, asked Belgium's prosecutor's office to arrest Puidgemont and four ministers in the dissolved Catalan government who ignored a court order to appear before a judge Thursday.
The charges include sedition, rebellion, misuse of funds, abuse of authority and contempt. The other four named in warrants are Toni Comin, Clara Ponsati, Lluis Puig and Meritxell Serret.
Belgian prosecutor Eric Van der Sypt said he has received the arrest warrants for Puigdemont and the others.
Van der Sypt told CNN in a telephone interview he would study the warrants and hand them over to an investigating judge within the next three days.
A statement from the Belgian federal prosecutor's office Saturday set out the next steps in the process, which could take weeks.
Once those named are found and brought before the judge, he or she has 24 hours to make a decision on what to do next, the statement said.
The judge can decide whether or not to issue an arrest warrant, and, if a warrant is issued, can decide whether the person concerned should be held or released under certain conditions.
If the judge issues an arrest warrant, then a court has 15 days to decide whether it is executed or not. The parties involved can then lodge an appeal, to be decided within 15 days, and potentially a further appeal to a higher court, also to be ruled on within 15 days.
The issuance of the warrant for Puigdemont's arrest was expected but still increases the tension between Catalan leaders and the Spanish national government, which so far has thwarted the region's drive to independence.
Puigdemont didn't appear and issued a video message calling the court's action "an attack on democracy."
He and some of his former ministers turned up in Brussels earlier this week after Spain's state prosecutor announced he would seek charges of rebellion, sedition and misuse of public funds against them.
The arrest warrant issued Friday also said Puidgemont would not be allowed to testify via videoconference from Belgium.