The regional government claimed that 90% of those who voted (estimated at 43% of the population) were in favour of independence - but Spain's constitutional court later ruled the vote illegal.
Police did not say exactly where Puigdemont, who had been living in Brussels since late October, was being held but the Spanish press said he was at a police station in the nearby town of Schuby.More news: Extent of US-China trade fight depends on Trump's goals
German police arrested Puigdemont earlier on Sunday as he crossed over by auto from Denmark, where had been visiting lawmakers.
German magazine Focus said Spanish intelligence informed the BKA federal police that Puigdemont was on his way from Finland to Germany.
In the meantime, Puigdemont was free to make trips to Denmark, Switzerland and Finland, as part of his effort to gain worldwide support for the secessionist movement.
Puigdemont was detained by German police Sunday who were executing an worldwide warrant issued by Spain on Friday.More news: Trump Signs Spending Bill, Averting Government Shutdown
Five other Catalan separatist leaders went into exile along with Puigdemont, who will now have to appear before a German judge who will decide if he is sent back to Spain to face trial.
The Schleswig prosecutor's office said "the question of whether Mr Puigdemont has to be taken into extradition custody, will then have to be determined by the higher regional court in Schleswig". After the report in the official newspaper of the Spanish government, the power in Catalonia passed to the government in Madrid.
Spain had originally asked for Puigdemont's extradition from Belgium after he moved there, but later withdrew the request until judge Pablo Llarena concluded his investigation this week.
The Supreme Court announced it would prosecute 13 key Catalan separatists for "rebellion", a crime that carries a maximum penalty of 30 years in jail.
The former Catalan regional president was at the time of his detention heading to Belgium, according to Puigdemont's spokesman Joan Maria Pique.More news: Gunman in France kills three, then takes hostages in supermarket
He gave up his quest to reclaim the presidency earlier this month.