The report, published on Tuesday, highlights abuse and torture carried out by CIA operatives at various locations around the world.
Shannon has often been cited as a location through which rendition flights were alleged to have travelled, but the Department of Justice said that was not the case.
In a statement it said: “The department has responded comprehensively over the years to allegations about rendition flights using Shannon Airport and has always stated that there is no evidence of rendition flights having transited through Shannon.
“It is recognised that a small number of commercially leased aircraft which have been involved in legitimate commercial activities may also have been involved at various other times in activities relating to extraordinary renditions.
“However, there is no evidence to suggest that any of these aircraft were carrying prisoners at any time when they transited through Irish airports.”
The department said a number of complaints that rendition flights were transiting through Shannon Airport had been received in the past number of years and had been the subject of investigation by gardaí.
“No evidence of rendition was disclosed in any of the investigations,” the department said.
“In some cases files were sent to the DPP but as there was no evidence of a breach of the criminal law there were no prosecutions.”
Roger Cole of the Peace and Neutrality Alliance said: “If you search the planes you would find the evidence but because you don’t search the planes you don’t find it. They deliberately do not search the planes.”
Separately, the Department of Transport said: “Aircraft landing at Irish airports for ‘technical’ stops for refuelling purposes are not required to have authorisation from the department or to notify the department.”