The announcement added to anger and dismay in a second straight night of demonstrations in the wealthy north eastern region, with protesters chanting and waving Catalan flags of red and yellow stripes with a white star.
Spanish prosecutors want to charge Puigdemont, holed up in Belgium, with rebellion, sedition and misuse of public funds. On Thursday the 54-year-old ignored a summons to appear before the same judge in Madrid.
A EU arrest warrant was also issued for four other Catalan ministers who failed to show up and are also thought to be in Belgium, a court statement said. They, like Puigdemont, were dismissed by Spain's central government a week ago.
On Thursday the judge had Puigdemont's deputy and seven other deposed regional ministers jailed pending a possible trial because of a risk that they might similarly abscond.
Speaking in an interview on Belgian television channel RTBF on Friday, recorded before the widely expected warrant was issued, Puigdemont said he was not hiding from “real justice” but from a “clearly politicised” Spanish legal system.
“I have told my lawyers to inform the Belgian justice authorities that I am completely at their disposal,” he said.
Belgian prosecutors said they would study the warrant and then give it to a judge.
Spain's worst political crisis in decades flared up over the staging of a Catalan independence referendum on October 1st despite a court ban. Spanish police tried and failed to stop it, in some cases firing rubber bullets.
An independence declaration by the Catalan parliament followed one week ago.
Spain's government responded by dismissing Puigdemont's government, imposing direct rule and calling fresh elections in Catalonia on December 21.
Twenty people including Puigdemont and the Catalan parliament speaker had been summoned for questioning on Thursday.
Puigdemont's Belgian lawyer Paul Bekaert, who has helped Basque separatists militants challenge Spanish extradition, said his client did not see the climate as “conducive to testifying”.
Late Thursday, as television footage showed police vans with flashing blue lights driving Puigdemont's former ministers to different prisons, furious Catalans took to the streets. About 20,000 people, according to police, demonstrated in the regional capital Barcelona, and thousands turned out again on Friday evening.
In Barcelona, people thronged outside the Catalan parliament chanting “Freedom for political prisoners”, “Occupying forces leave” and also “This Europe is a disgrace”. But there was also bemusement.
“It's brilliant that people are protesting, although it's a bit late,” demonstrator Melanie Ortiz, 27, told AFP.
'Not an internal matter'
Puigdemont has said that the situation “is no longer an internal Spanish affair”, calling on the international community to wake up to the “danger”.
But apart from Scotland's separatist First Minister Nicola Sturgeon criticising the “jailing of political opponents”, there are no signs that other countries' steadfast backing of Madrid is faltering.
Germany reiterated its support for the “unity and constitutional order of Spain” while a European Commission spokeswoman said it respects “fully” the independence of the Spanish judiciary.
“Spain has the rule of law and nobody can escape court decisions. There are international instruments to ensure that those who want to escape are placed at the disposal of the courts,” Spanish government spokesman Inigo Mendez de Vigo said.
The 7.5 million people of Catalonia, which until this past week had considerable autonomy, are fiercely proud of their language and culture but are also deeply divided about the wisdom of independence.
Spain's central bank warned Thursday of a possible recession in Catalonia. Unemployment there rose strongly in October. More than 2,000 firms have moved their legal headquarters elsewhere.
The separatist movement is also divided, although there are tentative signs that the latest events might galvanise its two main parties to fight the December election with a common list.
“It's absolutely indispensable that we have a joint strategy to battle the repression,” Sergi Sabria, a spokesman for the ERC party, told Catalunya Radio.
Peter Ceretti at the Economist Intelligence Unit said pro-independence parties might win the December election, as the jailed ministers could deliver an “important propaganda” boost.
Puigdemont said Friday he was “ready to be a candidate” in the election.
By AFP's Simon Sturdee with Alfons Luna in Barcelona