The authorities have confirmed claims in a report by Amnesty International (AI) that six suspected CIA flights landed in Switzerland.
The Federal Civil Aviation Office had previously refused to comment on the findings, only reaffirming that four flights were known to have touched down in Geneva.
There have been widespread allegations in the media and by non-governmental organisations that the CIA - the American intelligence service - ran secret jails abroad for terror suspects and flew some through European airports in so-called "rendition" flights.
The AI report, "Below the radar: Secret flights to torture and 'disappearance'", which was published on Wednesday, used data from the United States air authorities from 2001-2005 to track the alleged flights in Europe.
It found that three planes used by the CIA landed five times in Geneva and once in Zurich.
On Wednesday these claims were confirmed by the Aviation Office.
Dick Marty, a Swiss senator investigating allegations of secret CIA prisons on behalf of the Council of Europe, welcomed the report.
"Interestingly the research was done by civil society and not by the government," Marty told public radio.
"How come aircraft can fly through European airspace and land anywhere on the continent without any questions asked?" he added.
AI says it has records of nearly 1,000 flights directly linked to the CIA, most of which have used European airspace. Not all are said to have been carrying prisoners.
Amnesty said that most of these flights were by planes that appeared to be permanently operated by the CIA through front companies.
There are also records of another 600 flights made by planes used at least temporarily by the CIA, said the non-governmental organisation.
The CIA affair has had repercussions in Switzerland. In February the Swiss government granted permission for overflights by non-commercial US aircraft until the end of 2006, after receiving requested clarifications concerning CIA planes from Washington.
According to the government, the US authorities stated they had used neither Swiss airports nor Swiss airspace to transport prisoners.
The news came just days after a parliamentary sub-committee cleared the Swiss cabinet of having knowledge of such flights over Swiss airspace.
Only one suspicious case is still being investigated by the Swiss Federal Prosecutor's Office.
The CIA matter is also being investigated Swiss senator Dick Marty, on behalf of the Council of Europe. His interim report in January found European governments probably knew about CIA abductions and the transfer of detainees through European airspace.
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The Swiss Federal Civil Aviation Office has confirmed that six suspected CIA flights landed in Switzerland.
In addition, 76 flights were made over Switzerland by US planes suspected of being used by the CIA between 2001 and January 2006, according to the Aviation Office.
These were registered as non-commercial flights, it said.
Dick Marty, a senator for Switzerland's centre-right Radical Party, was appointed in November by the Council of Europe to probe allegations that the CIA set up secret prisons in eastern Europe to interrogate terror suspects.
In an interim report presented in January, he wrote that European governments probably knew about CIA abductions and the transfer of detainees through European airspace.
But he admitted that he had no concrete proof of CIA detention centres in eastern Europe or elsewhere.
Marty had also singled out the Swiss government as doing little to investigate, possibly to avoid a dispute with Washington.