Puigdemont was in Finland Friday when he learned Finnish police could be preparing to arrest him.
If a new leader is not elected by May 22, fresh elections will be triggered.
Dpa photos showed a van with tinted windows believe to be carrying Puigdemont as it arrived at the prison Sunday afternoon.
"We simply had the information that he was supposed to be in Germany or had entered the country", he said.
German police arrested Catalonia's deposed leader Carles Puigdemont on March 25, 2018, five months after he went into self-imposed exile in Belgium over his failed bid to break the region away from Spain.
Like Puigdemont, other politicians facing charges have left Spain to live in self-exile.
Mr Puigdemont is expected to appear later today or tomorrow before a judge, who will ask him if he agrees to be extradited to Spain.
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The detention of the fugitive ex-leader of secession-minded Catalonia has sparked mixed reactions in Spain.
This past week, a Spanish Supreme Court judge, Pablo Llarena, issued global arrest warrants for six Catalan politicians, including Mr. Puigdemont, and ordered five other Catalan politicians to be detained without bail.
Arrimadas said: "Puigdemont knew that fracturing Catalan society into two parts, spending public money on illegal activities, provoking a political and institutional crisis without precedents and confronting a 21st-century democracy of the European Union was going to have consequences".
At the same time in Girona, several dozen supporters of Catalonia's independence gathered under the representation of the Spanish government and, in protest at the arrest of Puigdemont, removed the flag of Spain and painted the walls of the building with yellow paint. State prosecutors in the northern town of Schleswig are now in charge, but they couldn't be immediately reached for further details.
Finland's National Bureau of Investigation (NBI) confirmed Saturday that it had received a European arrest warrant for "a Spanish citizen visiting Finland", but did not know the person's whereabouts.
Puigdemont's lawyer Jaume Alonso-Cuevillas, added on Twitter that he was picked up by German police as he was travelling back to Belgium to "present himself, as always, at the disposal of Belgian courts".
The European arrest warrant system in place since 2004 makes it easier for EU countries to demand the extradition from other EU states of people wanted for crimes, and removes political decision-making from the process. Separatists hold a majority in the regional parliament in the wake of elections in December.
He had wanted to be re-elected as Catalonia's regional president - albeit while remaining overseas to avoid arrest - but eventually was stopped by a Spanish court. Llarena ruled that a total of 25 Catalan separatists would be tried for rebellion, embezzlement or disobedience.