Mr Shatter has also confirmed that 10 allegations of such activity made by members of the public have been investigated in the past five years and no evidence of rendition was found.
Rendition is the practice of transferring individuals from one country to another by means that bypass all judicial and administrative due process.
Anti-war groups here have long maintained that Shannon has been used for extraordinary rendition operations by the US military and CIA.
Donegal Sinn Féin TD Pádraig MacLochlainn asked Mr Shatter whether he was aware of instructions being issued since 2004 that there was or is a policy not to search suspected rendition flights at Shannon Airport.
The minister told the deputy: “All complaints of this nature are dealt with in line with the advices provided by the Attorney General/Director of Public Prosecutions. An Garda Síochána are fully committed to investigate all alleged breaches of the criminal law including alleged offences involving the use of aircraft at Shannon Airport.”
John Lannon of Shannonwatch, a group which closely monitors US military aircraft at Shannon, said: “Members of Shannonwatch have been told on a number of occasions by gardaí that an “instruction” or “advice” has existed in relation to the searching of suspect rendition aircraft at Shannon Airport.
“We still have grave concerns about the failure to adequately investigate many of the complaints we have made over the years, and particularly the failure to search suspected rendition planes. Minister Shatter’s answer sheds very little light on why these searches didn’t take place,” he said.