The Federal Civil Aviation Office has confirmed that a small jet chartered by the CIA has flown over Switzerland 19 times since the start of 2003.
A plane was recorded on the day a radical imam was allegedly abducted in Italy and flown to Germany, but the aviation office does not know whether he was on board.
The revelations are the latest in a controversy that has exploded in Europe over allegations that the United States has held terror suspects and even tortured them in secret prisons in Europe.
The Council of Europe, the continent's human rights watchdog, has begun investigating, with Swiss lawmaker Dick Marty heading the probe.
Hassan Mustafa Osama Nasr, also known as Abu Omar, is an Egyptian cleric who was living in 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.
Thirteen months later he placed several phone calls from Egypt to his family and friends. Nasr claimed he had been taken by US agents and flown to Egypt where he had been severely tortured.
At the time of the calls he had been released on the orders of an Egyptian judge because of lack of evidence. Shortly after those calls were made he was apparently re-arrested and his whereabouts are no longer known.
Nasr was taken to the Italian-US air base at Aviano and flown by Learjet to Ramstein, Germany. A second plane then took him to Egypt.
The Federal Civil Aviation Office has confirmed that on February 17, 2003 a Learjet Model LJ-35, using the call sign "SPAR 92", twice flew over Swiss air space – from Aviano to Ramstein and back again.
SPAR is short for Special Air Resources, a military airlift service that uses Learjets and other executive-style jets to transport senior military officers and civilian VIPs.
The Federal Prosecutor's Office declined to comment.
The 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.
Foreign ministry spokeswoman Carine Carey told swissinfo that the Swiss embassy in Washington raised concerns with the US State Department in mid-November.
"These over-flights and landings in Switzerland are alleged to have transported prisoners, and this is one of the points [for which] we have asked for clarification," she said.
"The flights concerned have been declared as private flights and we have no knowledge about their aims or the identity of the passengers on board. Switzerland does not know if the CIA organised these flights – this is another question that has been addressed to the US.
"If these allegations were to be confirmed then Switzerland would condemn these practices, but there has been no concrete evidence so far."
swissinfo with agencies
The Washington Post reported on November 2 that the US is using "Soviet-style" prison camps to interrogate suspected terrorists in eastern Europe, most likely Poland and Romania.
US Secretary of State Condoleezza Rice labelled the movement of suspected terrorists as "renditions" in a speech on Monday.
The Federal Civil Aviation Office has confirmed that a small jet chartered by the CIA and suspected of ferrying political prisoners has flown over Switzerland 19 times since the start of 2003.
The European Parliament will decide next week whether to open an official inquiry into allegations that the United States has held terror suspects and even tortured them in secret prisons in Europe.
The Council of Europe, the continent's human rights watchdog, has already begun investigating, with Swiss lawmaker Dick Marty heading the probe.