Puigdemont requested that he be tried in absentia and testify via video, but the judge refused the request. Puigdemont and four of his lieutenants are currently in Brussels, Belgium.
Eight other Catalan ministers, including Puigdemont's former Vice President Oriol Junqeuras, are being held without bail in Madrid. Spain is seeking the arrests of Puigdemont and four other ministers who fled the country when the Catalan government was dissolved by Spanish Prime Minister Mariano Rajoy.
Rajoy dissolved the government in response to the Catalan Parliament formally voting to secede from Spain and declare Catalonia an independent republic on Friday. The new nation lasted all of three days.
Puigdemont and his fellow independence movement leaders face charges of rebellion, sedition, misuse of public funds and breach of trust.
"I will not run from justice. I will go to the justice authorities, but the real justice authorities," Puigdemont told Belgian state broadcaster RTBF in a Friday interview. "I have told my lawyer to tell Belgian justice authorities that I am completely ready to cooperate."
Rajoy has also called for snap parliamentary elections on December 21 to replace the dissolved Catalan Parliament. Puigdemont has called on his fellow Catalans to respect the results of the snap election."I am ready to be a candidate … it's possible to run a campaign from anywhere," Puigdemont told RTBF.
"We consider ourselves a legitimate government. There must be a continuity to tell the world what's going on in Spain … It's not with a government in jail that the elections will be neutral, independent, normal."
Catalonia's independent streak has been part of their national character for centuries. Their latest conflict with Madrid came to a head after an October 1 referendum in which over 90 percent of voters cast in favor of independence.
The Belgian prosecutor's office responded to the EU warrant by saying it would "study" it.