Amnesty International is calling for an overhaul of Ireland's procedures for granting overflight and landing permission to military aircraft.
The call follows yesterday's revelation that the US military transported a prisoner through Shannon Airport without seeking permission from the Irish Government.
The prisoner was a US soldier convicted of a minor breach of the US military code and his transfer through Shannon was not connected to the controversial CIA rendition scheme.
Foreign Affairs Minister Dermot Ahern said the US Embassy had informed him of the breach, which he described as "inadvertent".
However, the Irish branch of Amnesty International said today that it appeared a cleaner had actually first raised the alarm and notified the airport authorities.
Amnesty said the incident highlighted the need for Ireland to regain control over the use of its airspace and territory by US military aircraft.