Dogan Akhanli, a German intellectual of Turkish origin who writes on Turkey's record on human rights, was arrested in Spain on Saturday at Ankara's request, the foreign ministry said in Berlin, adding that it opposed any extradition of the writer.
The arrest was initially announced by German Green MP Volker Beck, who described it as a politically-motivated move by Turkish president Recep Tayyip Erdogan.
A foreign ministry official later confirmed the arrest. The ministry has asked Madrid not to extradite Mr Akhanli to Turkey, and that its embassy be allowed to provide consular assistance "as quickly as possible", the official said.
The Spanish interior ministry could not immediately be reached for comment.
Mr Akhanli's local newspaper, the Koelner Stadt-Anzeiger in western Germany, said the Turkish-born writer was arrested in the southern Spanish town of Grenada on Saturday morning. The accusations against him were unknown.
Spanish police had a so-called red notice - an alert circulated by Interpol that is roughly equivalent to an international arrest warrant.
Mr Akhanli's website says he was born in northeastern Turkey in 1957, moved to Istanbul at the age of 12 and was held as a political prisoner from 1985 to 1987, when he was tortured.
He moved to Cologne in the 1990s, was stripped of his Turkish citizenship and became a German citizen in 2001, it says.
The arrest shows that Mr Erdogan is seeking to "extend his power beyond his country's borders, to intimidate critics and to pursue them around the world", Mr Beck charged.
Mr Akhanli has written about the killing of Turkish-Armenian journalist Hrant Dink, who was murdered in 2007, and about the killing of Armenians under the Ottoman Turkish empire.
Between half a million and 1.5 million Armenians were killed between 1915 and 1917 - a bloodletting that Armenia and Western historians describe as genocide.
Turkey vehemently objects to the term. It argues that 300,000 to 500,000 Armenians and as many Turks died in civil strife when Armenians rose up and sided with invading Russian troops.
Mr Akhanli was arrested in 2010 on his arrival in Istanbul airport for alleged implication in an armed robbery in 1989. He was released four months later and then declared innocent, before a court of appeal ordered new proceedings against him.
German Green MPs took up his cause, saying he had been a victim of political persecution.
Relations between Germany and Turkey have been at a nadir since a failed putsch against Mr Erdogan in July 2016.
Turkish accusations include the charge that Germany has given refuge to wanted Kurdistan Workers' Party (PKK) militants and suspected coup plotters.
Turkish-German journalist Deniz Yucel, the Istanbul correspondent of newspaper Die Welt, has been held in jail in Turkey since February ahead of trial on terror charges.