By Craig Whitlock
Washington Post Foreign Service
Wednesday, January 31, 2007; 3:04 PM

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.

Christian Schmidt-Sommerfeld, the chief prosecutor in Munich, said 13 CIA operatives were wanted on charges of kidnapping and inflicting bodily harm on Khaled el Masri, a German citizen of Lebanese descent. Masri has said he was detained by border guards while en route to a holiday in Macedonia and was handed over in January 2004 to the CIA, which secretly flew him to Afghanistan and interrogated him about his alleged ties to Islamic radicals in Germany.

After five months in captivity, Masri was flown back to the Balkans and dumped on a hillside in Albania. German prosecutors were skeptical at first after he came to them with a bizarre-sounding story about how he was kidnapped, but they later corroborated many parts of his account.

At a news conference in Augsburg, Germany, Masri's attorney called the arrest warrants "a great success" and said his client was "very satisfied" with the outcome of the investigation.

Yet the attorney, Manfred Gnjidic, said he realized it was doubtful that German authorities would be able to track down any of the suspects and bring them to trial.

"It is not to be expected that the agents, against whom the arrest warrants were issued, will come to Europe and let themselves be arrested," Gnjidic said.

Robert Wood, a spokesman for the U.S. Embassy in Berlin, declined to comment on the arrest warrants. The CIA also declined to comment.

In September, German prosecutors said they had received from Spanish investigators a list of CIA operatives suspected of involvement in Masri's disappearance. According to hotel records and flight logs, the CIA officers had stayed on the Spanish island of Mallorca in December 2003 before flying aboard a privately chartered Boeing 737 to Skopje, Macedonia, where Masri was picked up and transferred to Afghanistan.

Prosecutors in Munich did not identify any of the suspects named in the arrest warrants and released few other details about the probe. Investigators have said they believe most of the suspects used aliases. Three are believed to be pilots who worked on a contract basis for the CIA.

Around the time of Masri's release, U.S. diplomats privately informed Otto Schily, then Germany's interior minister, that a German citizen had been mistakenly detained under the CIA's program of "extraordinary renditions," or the extrajudicial abduction of Islamic radicals who are secretly taken to allied countries for interrogation.

In December 2005, German Chancellor Angela Merkel said U.S. Secretary of State Condoleezza Rice acknowledged in a meeting in Berlin that Masri had been "erroneously taken." But Rice and other U.S. officials have denied any fault or responsibility in the case.

A year later, in December 2006, Rice was asked by a reporter in Washington if the U.S. government owed Masri an apology. Rice declined to issue one. "We have tried to deal with this case in a way that is responsible and -- you know, that's all I'm going to say about this case," she said.

Masri filed suit against the U.S. government in federal court in Alexandria in December 2005, but his complaint was dismissed last May on grounds that it could divulge CIA secrets and damage U.S. national security operations. Masri appealed the decision to the U.S. Court of Appeals for the 4th Circuit in November.

Staff writer Glenn Kessler contributed to this report from Washington.