Loganair has switched expansion from Edinburgh to Glasgow airports in protest at a new “congestion charge” for morning rush-hour flights.
The airline, which operates to the Highlands and Islands under a Flybe franchise, also accused the east coast airport of not being interested in smaller aircraft.
From next April, Edinburgh will introduce an extra £200 charge for aircraft operating between 6:45am and 7:15am.
Airlines will also be charged a further £2 per passenger on international flights between these times from June to August.
Scotland’s busiest airport, which handles 12 million passengers a year, will also hike landing charges across the board by 8 per cent in April, compared to by around 1 per cent at Glasgow Airport.
Loganair has axed an Edinburgh-Stornoway flight as a result, and MSPs fear other island services could follow suit if the congestion charge is extended.
That sort of level of charges for the size of aircraft we operate is not tenable
The airline will instead increase its seat capacity on flights from Glasgow by 20 per cent, with a new route to Bergen in Norway, extra flights to Islay, Kirkwall and Manchester, and larger aircraft on the Stornoway and Sumburgh routes.
Managing director Jonathan Hinkles said: “We have deliberately directed growth away from Edinburgh to Glasgow.
“That sort of level of charges for the size of aircraft that we operate to Stornoway is not tenable.
“Ironically, it will free up a slot for a larger aircraft, which will make queues worse.
“There is a question over what they want their airport to look like, in terms of size of aircraft, because they need smaller planes to feed into other routes.
“If you are not a 150-seat jet, they don’t seem to be interested.
“We have a sensible, open dialogue with the management at Glasgow Airport. We don’t have that with Edinburgh.”
Shetland MSP and former transport minister Tavish Scott said: “Passengers from other parts of Scotland seem to be forgotten about by Edinburgh Airport in the pursuit of large jets from the Middle East and United States.
My concern is the new charging scheme is the thin end of the wedge and could be extended, which could affect more flights.”
Edinburgh Airport said the extra £2 charge would be offset by fees being cut by £1 per passenger on international flights between November and March.
A spokesman said: “In next year’s peak period, we have demand for more scheduled departures than it is physically possible for us to accommodate on the existing flight paths.
“We cannot tell airlines when they can take off and land, so a small congestion charge option - where airlines have the choice to pay if the departure time is critical to them or be rescheduled out of peak time – will come into play.
“We have engaged with Loganair to try to find an equitable solution – something we have successfully found with other carriers.
“We respect its decision to not move their scheduled departure time by up to 15 minutes and look forward to continuing to do business with them in 2017.”