The US Secretary of State, Condoleezza Rice, has denied that the US uses CIA flights to transport terror suspects to other countries for torture.
However, Ms Rice said that suspects were moved by plane under a process known as rendition. She was speaking in the US, before departing for a visit to Europe.
The former President of Ireland and former UN High Commissioner for Human Rights, Mary Robinson, has said it needed to be established how torture was defined both inside and outside the US.
Information obtained by RTÉ under the Freedom of Information Act indicates there may have been a total of 38 landings of CIA flights at Shannon Airport, mostly since 2002.
But there is no indication whether terror suspects were on board those flights.
The Council of Europe is investigating 31 flights through European airports which are believed to have been operated by the CIA.
Among them is a flight through Shannon last year that may have been used to carry prisoners from Afghanistan to a secret prison in Romania.
The council has invoked its powers under the European Convention on Human Rights to ask its 45 members (including Russia) for information on suspicious CIA activities, as part of its own investigation into the affair.
It is only the eighth time since the convention came into force in 1953 that this procedure has been used.
Ms Rice is expected to face questions over reports of secret CIA prisons, as well as the secret flights, during her tour of Europe. She will visit Berlin, Bucharest, Kiev and Brussels.
EU concerns
Last month, the EU wrote to Ms Rice expressing misgivings over the alleged jails and reports that CIA planes carrying detainees had stopped in EU countries.
The controversy has been simmering since allegations emerged that terror suspects had been flown via European airports to countries like Egypt, Syria, Morocco, Uzbekistan and Jordan, all thought to practice torture.
There were other media reports that two Eastern European countries - allegedly Poland and Romania - had provided interrogation centres for the CIA.
The issue has surfaced in Italy, Germany and Sweden.
In Sweden a parliamentary investigation concluded that the arrest of two Egyptians at Stockholm airport, and who were allegedly stripped and hooded and put on a CIA flight en route to Cairo, was a violation of Swedish law.
The two men later complained to the Swedish ambassador to Egypt that they had been tortured.
RTÉ News has learned that the plane which took them there, which had the registration number N379P, had landed at Shannon 13 times between 2002 and 2003.
The plane was then re-registered as N8068V and landed three times in 2003 for refuelling. However, the N379P registration turned up in Cork once this year.
In another case, a gulfstream jet (N85VM) allegedly involved in the CIA kidnapping of an islamic cleric in Milan landed in Shannon eight times.
A further plane, N313P, claimed by Newsweek magazine as being part of the CIA's covert network, landed 13 times at Shannon.
The Department of Foreign Affairs has said that these planes were registered as civilian aircraft so there was no requirement for advance notice, and that no inspections were carried out.
