The MoD has denied that a major military exercise was to blame for an SNP MP missing a series of Brexit votes in the House of Commons.
Western Isles MP Angus MacNeil said his Loganair flight from Barra was cancelled on Monday because of the Joint Warrior exercise.
Loganair also suggested the exercise had caused the closure of the route.
But in a statement released on Tuesday, the MoD insisted that this was not the case.
An MoD spokesman said: “The nature of the delay to yesterday’s Loganair flight from Barra to Glasgow was not due to a military exercise.
“The altitude that the flight wished to transit was below the airspace restriction, therefore from a military point of view there was no reason why the Loganair flight could not have operated.”
Mr MacNeil had been due to fly to Glasgow before catching a flight to London in time for the latest series of indicative votes on Brexit.
Last week, he and fellow SNP MP Pete Wishart rebelled against the SNP leadership by abstaining in a vote on whether there should be another EU referendum.
The rest of the party’s MPs voted in favour of the option – and backed it again on Monday. The proposal was defeated by 12 votes.
The UK-led Joint Warrior exercise is currently being held off the coast of Scotland, and involves more than 10,000 military personnel, 35 warships, five submarines and 59 aircraft from Nato nations and Australia.
In a tweet sent on Monday, Mr MacNeil said the Barra flight had been cancelled as there was a “Military No Fly Zone” (MNFZ) in the Minches and Hebrides, and that the military “didn’t warn civil flights”.
He added: “I will not be in Westminster to vote at 8pm to 8:30 Brexit division. Airport staff cursing the MNFZ”.
The MP has been asked for a response to the MoD statement.
Loganair’s managing director Jonathan Hinkles said on Monday: “The Joint Warrior military exercise results in closures at short notice of certain areas of airspace, including that route used by our Twin Otter aircraft to and from Barra.
“This can lead to unexpected flight delays or cancellations which are regrettable in terms of their impact on our customers, but unavoidable from the standpoint of safety and security, which are always our absolute priorities.”
The airline said it had no further comment to make to Tuesday.