Puigdemont will "remain in detention for the time being, until a decision is made concerning the extradition procedure," the regional court in Kiel, northern Germany, announced Monday, a day after Puigdemont was arrested.
The former Catalan leader's detention in Germany, which sparked angry protests back in Catalonia, comes five months after he went on the run as Spanish prosecutors sought to charge him with sedition and rebellion in the wake of a vote by the Catalan parliament to declare independence.
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The court in northern Germany turned down a request from Puigdemont's legal team for him to be released pending the extradition decision by German authorities.
He was arrested on Sunday after he crossed the border into Germany from Denmark, under a European warrant issued by Spain. According to Puigdemont's lawyer Jaume Alonso-Cuevillas, he was on his way back to Belgium, where he fled after Spanish authorities moved to impose direct rule over Catalonia.
His detention marks the latest chapter in a secession saga that has bitterly divided Catalans and triggered Spain's worst political crisis in decades.
Protest in Barcelona
A decision on extradition must normally be made within 60 days under German law. A spokeswoman for the prosecutor's office for Schleswig-Holstein state told AFP it would "probably not come this week" ahead of the four-day Easter holiday.
In Barcelona Sunday, Catalan police in riot gear shoved and hit demonstrators with batons to keep the crowd from advancing on the Spanish government's representative office in the capital of Spain's wealthy northeastern region.
Officers fired warning shots in the air to try to contain the demonstrators, who pushed large recycling containers towards police. Some people threw glass bottles, cans and eggs at police.
About 90 people were slightly injured during the protests in Barcelona, including 22 police officers, emergency services said.
'Solution can be found'
The case lands an unwanted diplomatic hot potato in German Chancellor Angela Merkel's lap less than two weeks after her new government was sworn in.
Her spokesman insisted Monday that the decision on Puigdemont's extradition rested solely in the hands of the German regional justice authorities.
Spain's deputy prime minister Soraya Saenz de Santamaria welcomed the arrest as "good news", saying: "No one can make a mockery of the courts forever".
Protesters in Barcelona saw the move as a provocation while Catalan parliament speaker Roger Torrent appealed for calm in an address broadcast on regional television.
Aside from Puigdemont, nine other Catalan separatist leaders are in jail in Spain over the region's failed bid for independence.
His arrest came two days after Spain's supreme court issued international arrest warrants for 13 Catalan separatists including Puigdemont and his nominated successor Jordi Turull.
The court said they would be prosecuted for "rebellion", a charge which carries a maximum sentence of 30 years in prison.
Twelve more face less serious charges such as disobedience.
Issuing the warrant for Puigdemont on Friday, Judge Pablo Llarena accused the ousted Catalan leader of organising an independence referendum in October last year despite a ban from Madrid and the risk of violence.
That vote had been swiftly followed by the Catalan parliament's declaration of independence on October 27th.
'Revenge and repression'
Puigdemont had been visiting Finland since Thursday, but slipped out of the country before Finnish police could detain him.
In Geneva, the UN Human Rights Committee said it had registered a complaint from Puigdemont, which his lawyer has earlier said concerned Madrid violating Puigdemont's right to be elected and his freedom of expression and association.
Elsa Artadi, a lawmaker with Puigdemont's Together for Catalonia party, said he should fight his extradition.
"Spain does not guarantee a fair trial; only revenge and repression," she wrote on Twitter.
While separatist parties won Catalonia's regional elections which were called by Madrid in December, they have been unable to elect a president and form a government as they have picked candidates who are now either in exile, in jail or facing prosecution.
After Puigdemont was forced to withdraw his bid for the presidency as he could not return to Spain without facing arrest, another pro-independence leader Jordi Sanchez followed suit when a judge refused to let him out of jail to be sworn in. The third candidate, Turull, was placed in custody on Friday.
Fresh regional elections will be triggered if a new leader is not elected by May 22nd.