Permission to carry munitions or dangerous goods on civilian aircraft through Ireland or Irish airspace must be sought from the Department of Transport.
Last year, the number of applications for such exemptions was 1,393, with a total of 1,382 permits being issued, the vast majority to planes landing at Shannon.
Responding to parliamentary questions from Sinn Féin TD Pádraig Mac Lochlainn, Mr Varadkar confirmed that most of the requests to his department were made by US civil airlines. Omni Air International operates up to four flights a day carrying US troops through the airport, mostly going to and from Kuwait and Kyrgyzstan.
A spokesman for Shannonwatch, a group which closely monitors US activity at Shannon, said: “Like Kuwait and Kyrgyzstan, Ireland and Shannon have now become staging posts for US invasions and occupation.
“These figures make a mockery of the notion of Irish neutrality, and show that successive governments have relinquished all interest in maintaining an independent Irish foreign policy.”
Mr Varadkar also said “under 250,000” US troops transited Shannon last year although he failed to confirm the exact total.
Meanwhile, Alan Shatter, the defence minister, has confirmed that the cost of Garda protection for US aircraft at Shannon Airport for 2011 was almost €1m while the total cost of assistance provided by the Defence Forces to the gardaí at Shannon for the year was €259,739.