The Council of Europe claim that Ireland colluded with the United States in the unlawful transfer of detainees was dismissed by Minister for Transport Martin Cullen.
"As I repeatedly stated in the House, the Government has received categorical and unambiguous assurances from the US authorities that prisoners have not been transferred through Irish territory, and would not be without our permission."
Labour's foreign affairs spokesman, Michael D Higgins, suggested the Minister was not in a position to say whether it had happened because the planes had not been inspected.
"He does not inspect any plane, and he does not know what went through Shannon."
Mr Cullen said that the "assurances on which the Government rely relate to a categorical factual statement that no individuals are being transferred through Irish territory".
He said that before the matter developed into a big international issue, the Government had very specifically spoken to the US authorities.
"Ireland was one of the few countries to get an absolutely categorical factual statement from the Americans to the effect that no such practice has taken place as regards the movement of prisoners or rendition issues, and this country."
Replying to special notice questions, Mr Cullen said the comprehensive nature of Ireland's investigation of such matters had already been endorsed by the secretary general of the Council of Europe, when he adjudged Ireland's submission as one of only eight out of 45 submissions not to require further clarification.
Fine Gael spokesman Bernard Allen said there was a distinct impression that the Government had turned a blind eye to traffic through Shannon airport.
"Will the Minister now ensure that all flights using Irish facilities, be they commercial or privately-owned aircraft, provide full passenger listings to the relevant Irish authorities?"
Mr Cullen said there was no question of Ireland turning a blind eye to such matters.
"Ireland has been to the forefront in making our position absolutely clear to the US."
Sinn Féin's Aengus Ó Snodaigh said that a host of reputable human rights organisations and individuals had demanded an end to Irish complicity in the "US's illegal rendition programme".
Mr Cullen said he utterly rejected the assertion that there was collusion between the State and the US regarding the rendition of prisoners. "The assertion is totally untrue and has no foundation."
Green Party leader Trevor Sargent said that an Amnesty International report had stated that between September 2001 and September 2005, Shannon airport was used on 50 occasions by CIA planes disguised as commercial airlines.
"The Minister should take on board the legal reality. His statements to date have been akin to those of a priest in church trying to tell us about the resurrection of Jesus Christ. That it is a matter of faith but the matter in hand is one of law."
Mr Cullen said that Mr Sargent seemed to ignore entirely that the comprehensive nature of Ireland's investigation had already been endorsed by the secretary general of the Council of Europe.
