BERLIN, Jan. 31 — German prosecutors on Wednesday said they have issued arrest warrants for 13 CIA operatives suspected of kidnapping a German citizen in the Balkans in 2004 and taking him to a secret prison in Afghanistan before realizing several months later that they had the wrong person.

The German arrest warrants, filed in Munich, are the second case in which prosecutors have filed criminal charges against CIA employees involved in counterterrorism operations in Europe. European investigators acknowledge that it is highly unlikely the U.S. spies — most of whom worked undercover or using false identities — would ever be handed over to face trial. But the prosecutions have strained U.S.-European relations and underscored deep differences over how to fight terrorism.

Italian prosecutors have also issued arrest warrants for 25 CIA operatives and a U.S. Air Force officer, alleging that they kidnapped an Egyptian-born radical cleric off the streets of Milan in 2003 and took him to Cairo, where he claims he was tortured. A court in Milan is presently considering whether to press ahead with indictments of the CIA officers and try them in absentia later this year.

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