The Irish Air Line Pilot's Association (IALPA) says pilots must remain in charge of an aircraft security even if air marshals are introduced to passenger flights.
IALPA's safety director, Mr Conor Nolan, said pilots will be seeking assurances that under any new plan the captain will maintain "ultimate authority" for the safety of the flight.
Speaking on RTÉ radio this morning, Mr Nolan said he would be raising a number of concerns with the National Civil Aviation Security Committee.
The Committee - which includes the secretaries-general of the Departments of Justice and Defence, the Garda Commissioner and the Defence Forces Chief of Staff - is considering new security measures on passenger airlines.
At least three European countries are opposing the American authorities' insistence on having armed guards on some transatlantic flights.
Sweden, Denmark and Portugal say they will not authorise loaded guns on their planes and therefore armed guards will not be allowed.
British airline pilots' union Balpa was today meeting the country's transport secretary Mr Alistair Darling to seek an all-embracing agreement on the controversial scheme.
Mr Darling yesterday dismissed as "complete rubbish" a suggestion that recent British Airways transatlantic flights had been grounded to force the airline to accept sky marshals.
The BA223 flight from Heathrow to Washington, DC, was delayed for a third day running yesterday over terrorism fears.
Additional reporting by PA
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