Amnesty International says it has collected evidence that three aircraft involved in US rendition flights had links to Shannon Airport.
As part of a week of events to mark International Day Against Torture, the human rights group has published a report on Europe's role in rendition and secret detention.
In their latest report Amnesty International accuses a number of European states of either turning a blind eye to rendition or actively participating in it.
The report highlights six cases, three of which have links to Shannon Airport.
In the case of one man, Abu Omar, the report says the aircraft that took him from Germany to Egypt eventually returned to the US through Shannon.
In the case of another man, Khaled al-Maqtari, the report says the plane which took him from Iraq to Afghanistan had previously stopped in Shannon.
And in a third case, Amnesty says the aircraft that took Khaled el-Masri from Macedonia to Afhganistan had also stopped at Shannon.
In response, the Department of Foreign Affairs said the Government is completely opposed to the practice of the rendition of prisoners.
In a statement, it said no evidence has ever been produced that any person has ever been subject to extraordinary rendition through Ireland.