Foreign Affairs Minister Simon Coveney says he has total respect for all military personal.
The Irish Times reports Simon Coveney had tense exchanges with an Air Corps pilot in 2015 when he was Minister for Defence and trying to get to a meeting.
Internal emails are said to show the Air Corps being "very unhappy" with the minister's intervention.
Responding this morning, Minister Coveney said: "I have the utmost respect for all military personnel - and I think that my time in the Department of Defence would show that.
"I don't want to add to that story any further, apart from to add that I have total respect for the judgement of military personnel."
Fianna Fáil's Michael McGrath, however, described the report as 'extraordinary', and says Simon Coveney needs to outline what happened.
Speaking on Newstalk Breakfast, Deputy McGrath argued: "It would appear that there are documents and emails - so clearly the issue escalated to quite a serious degree.
"I think for his own sake he should come out and clarify whether or not he did challenge the pilot, because there's an issue raised about the tone of the exchange as well."