The Department of Transport has said it was "dissatisfied" that Shannon airport had been used by a cargo aircraft carrying Apache attack helicopters between the US and Israel in February.
A spokesman said the department would be reminding aircraft operators that such military equipment was considered to be weapons, thus their carriage through Irish airports or airspace was prohibited unless an exemption was granted.
The aircraft, which stopped overnight en route from the US to Israel, was carrying three Apache attack aircraft.
The Israeli government has a fleet of the Apache attack aircraft. In February, one such helicopter killed two people in Gaza city after it hit two cars carrying Islamic Jihad militants.
The department spokesman said the cargo aircraft was not due to land at Shannon on its outbound journey as it was scheduled to fly via Iceland.
"Our inquiries have established that a last-minute decision was made by the operator to route the aircraft through Shannon," he added. "We are advised that this was done so that a technical problem could be attended to at the company's maintenance base at Shannon.
"The notification of the change of routing was not sent to the Department of Transport."
The company in question, Volga-Dnepr, usually provided a note to the Department of Transport in advance of flights operating through Ireland, he said.
The department was notified that the aircraft had been due to stop over at Shannon on the return leg of the journey when it would have been empty.
However, the spokesman said that it had subsequently learned "that helicopters were in fact carried on the return flight through Shannon on 28th February".
Volga-Dnepr believed it did not need an exemption as there were no weapons or munitions on the helicopters.
"The Department of Transport has informed the company that the helicopters themselves and similar military equipment whether air-, sea- or land-based are considered to be weapons," the spokesman said.
The department would have to consult the departments of foreign affairs, justice and defence and the Irish Aviation Authority before granting an exemption under the Air Navigation (Carriage of Munitions of War, Weapons and Dangerous Goods) Order, 1973.
"If any of those agencies objects to the exemption being given, then the department will refuse to grant an exemption," the spokesman said.
Green Party chairman John Gormley called for an investigation into the matter by the Joint Oireachtas Committee for Foreign Affairs.
On Saturday, the Irish Independent reported that the Department of Transport and the Department of Foreign Affairs had initially denied knowledge of the flight when questioned by the newspaper.
Mr Gormley said this denial raised serious questions about the role of the Department of Foreign Affairs.
If it was established that it had covered up the information, "then the Minister for Foreign Affairs will have no option but to resign", Mr Gormley said.
The cargo aircraft landed at Shannon hours before the US president, George W Bush, made a refuelling stopover at the airport.
