Mr Shatter was responding to questions from Independent TD Clare Daly, following confirmation last month that a heavily armed US military plane landed at Shannon in contravention of its landing conditions.
The US Air Force AC130 plane was carrying a powerful, side-mounted, 30mm cannon when it transited Shannon on Sept 5 last.
Anti-war groups have made repeated formal complaints and requests for US aircraft at Shannon to be searched to ensure they are fully compliant with their strict landing conditions.
Mr Shatter said: “An Garda Síochána remain fully committed to investigate all alleged breaches of the criminal law, including alleged offences involving the use of aircraft at Shannon Airport or other Irish airports.”
He added, however: “I would point out, for the sake of clarity, that the Garda Síochána has no role in relation to the inspection of foreign State or military aircraft which, in accordance with international law, enjoy sovereign immunity.”
ShannonWatch spokesman John Lannon said: “This means that the Irish government is allowing the US military to take whatever or whoever they want through Ireland, regardless of the human rights, security and other consequences.”
According to Mr Shatter: “The Garda Síochána has statutory powers of search and entry available to it under various legislative provisions and these apply to aircraft as much as to any other type of private property. However, these powers may only be exercised in circumstances where a member of the Garda Síochána reasonably suspects that an offence has been or is being committed.”
But Mr Lannon said there “there have been plenty of incidents in which there were reasonable grounds to suspect involvement in torture-related offences and these have not been investigated.”
The minister also said gardaí fully investigated a number of allegations of unlawful activity at airports and files have been submitted to the DPP in some of these cases. The Government also made this claim in its report to the fourth periodic review under the International Convention on Civil and Political Rights.
At that time they noted 17 complaints were received by gardaí regarding alleged rendition flights to/from Shannon Airport, however they could only confirm seven of these were investigated, Mr Lannon added.
Shannonwatch has called on the Department of Justice to make the outcomes of the investigations of all the complaints known, or if no investigations took place, to explain why.