The Federal Prosecutor's Office has opened a criminal investigation into alleged overflights in Swiss airspace of CIA planes carrying detainees.
The investigation will seek to establish whether the United States committed illegal acts on Swiss territory.
"The investigation is in connection with the alleged CIA overflights," Hansjürg Mark Wiedmer, a spokesman for the prosecutor's office, confirmed.
The investigation was launched earlier this week, but prosecutors are aware of the difficulties they will probably face in obtaining information from Washington, Wiedmer said.
The Swiss foreign ministry has twice sought clarification about four alleged CIA flights touching down at Geneva airport and some 30 other flights passing through Swiss airspace. But Washington has yet to respond to the questions.
A spokesman for the US Embassy in the Swiss capital, Bern, said a response was still pending.
According to the Federal Civil Aviation Office, US-registered planes suspected of being used by the CIA, crossed Swiss airspace on at least 73 occasions since 2001.
One plane registered to the US Department of Defense flew across the country twice on February 17, 2003, on a flight from Ramstein, Germany, to Aviano, Italy, and back again to Ramstein.
Italian prosecutors have reportedly identified the plane as being used to fly a radical imam, allegedly abducted by American agents that day in Milan, to Ramstein from where he was taken on to Cairo.
Hassan Mustafa Osama Nasr, also known as Abu Omar, is an Egyptian cleric who sought asylum in Italy after his Islamic organisation was declared illegal by the Egyptian government in the 1980s.
On February 17, 2003 he was abducted as he walked to his mosque in Milan for noon prayers.
Italy has issued arrest warrants for 22 suspected CIA agents accused of involvement in the kidnapping.
Nasr's Egyptian defence lawyer claims the cleric was tortured after he arrived in Egypt.
Wiedmer said the timing of the flights and the alleged kidnapping played a role in the opening of the Swiss investigation.
The Council of Europe, the continent's human rights watchdog, has begun investigating reports that the CIA set up secret jails in some European nations and transported terror suspects by covert flights.
Swiss lawmaker Dick Marty is heading the probe. Marty had singled out the Swiss government as doing little to investigate, possibly to avoid a dispute with Washington.
Several other investigations are under way into whether European countries may have hosted secret CIA-run prisons.
Also covered in these investigations are allegations that European airports and airspace were used for CIA flights in which prisoners were tortured or transported to countries where torture is practiced.
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The Federal Prosecutor's Office has decided to open an investigation into CIA overflights and landings in Swiss airspace and territory.
Switzerland has already asked Washington for explanations about four landings at Geneva airport and 30 flights in Swiss airspace.
On November 2, the Washington Post published an article accusing the United States of using secret prison camps in eastern Europe to interrogate terror suspects.