The Government has said it was unacceptable that the US authorities did not seek the required consent before a civilian aircraft landed at Shannon Airport last Sunday carrying a US marine who was in military custody.
The Minister for Foreign Affairs, Dermot Ahern, said the Government is seeking a full written report from the US Embassy on the matter.
He said the Government regarded it with the gravest concern.
The minister said he had summoned the US Ambassador for a meeting at Iveagh House where the ambassador had conveyed his regret for the breach of procedures, which he blamed on an administrative error.
Mr Ahern said the matter had been discussed at Cabinet this morning.
The Omni Air International aircraft landed at Shannon to refuel en route from Kuwait to Wright-Patterson AFB, near Dayton, Ohio.
It was carrying 180 unarmed US military personnel.
It is understood that a cleaner who boarded the aircraft discovered the prisoner.
Mr Ahern said the incident had no connection with allegations of extraordinary rendition.