Ireland is contravening international law by allowing its territory to be used to facilitate extraordinary rendition, Amnesty International has claimed.
In the report Khaled al Maqtari describes a regime of beatings, sleep deprivation and induced hypothermia
The human rights group based its allegation on a report into the case of a Saudi man who was held without charge in secret CIA prisons for over two-and-a-half years.
Khaled al Maqtari claims he was subjected to torture and other forms of cruel and inhumane treatment while being held in unknown locations and in isolation from 2004 to 2007.
An Amnesty report into his case found that Shannon airport was used as a refuelling stop by the plane that took him from Iraq - where he was initially arrested - to Kabul, where he was incarcerated in a CIA prison.
Amnesty International Irish section executive director Colm O'Gorman said: "There can no longer be any doubt that Shannon is being used by those involved in kidnapping and torture, dressed up as part of a war on terror.
"Recent revelations that the US used British territory to transfer kidnapped prisoners despite assurances similar to those given to Ireland that our territory was not being used to commit such gross violations of international law should be of very grave concern to the Irish Government."
At the beginning of his 32-month confinement, Mr al Maqtari was taken to Abu Ghraib prison in Iraq. After nine days of interrogation in Abu Ghraib, he was taken by plane to a secret CIA detention facility in Afghanistan, were he was held for a further three months.
Flight records obtained by Amnesty International corroborated that a jet allegedly operated by a CIA front company left Baghdad International Airport nine days after his arrest, heading for Khwaja Rawash airport in Kabul.
"This same jet, registered at the time as N379P, had left Shannon Airport on January 20th, 2004 en route to Baghdad where it collected Mr al Maqtari," Mr O'Gorman said.
A statement, issued this evening, on behalf of Minsiter for Foreign Affairs Dermot Ahern said: "The Government is totally opposed to the practice of extraordinary rendition and we have reiterated our position on numerous occasions, both domestically and internationally."
"The Government has received specific assurances from the US authorities that no prisoners have been transferred through Irish airports, nor would they be, without our permission.
"The assurances are of a clear and categoric nature, relating to facts and circumstances within the full control of the US Government.
"They have been confirmed at the highest level, including by President Bush to the Taoiseach and by Secretary of State Rice to myself," Mr Ahern said.
But Labour leader Eamon Gilmore said the Amnesty report strongly reinforces the case for the Irish authorities insisting on the right to inspect aircraft suspected of being involved in extraordinary rendition.
"It is difficult to dispute the assessment of Amnesty that Ireland is contravening international law by allowing its territory to be used to facilitate extraordinary rendition," Mr Gilmore said.
"Indeed, I would go further and say that the failure to assert our right to check these planes leaves Ireland potentially complicit in the kidnap, detention and torture of people against whom no charges have been proven and who, in many cases, are totally innocent."
Amnesty believes that at least three dozen prisoners are still being held in the secret CIA prison network.
The Irish Anti-War Movement is organising a protest against the Iraq war in Dublin on Saturday to mark the 5th anniversary of the US-led invasion
The demonstration, which is scheduled to take place in Parnell Square from 1pm, is part of the World Against War global protests in over 50 cities.
