The revelation comes days after William and Kate were praised for using an economy flight from Norwich when Prince Harry and Meghan have been criticised for a series of private jet trips.
It is understood the empty flights made by the two 49-seat aircraft cost around four tonnes of carbon.
An aviation source with knowledge of what happened said the plane which normally flies the route had been replaced by a Flybe-branded aircraft in an attempt to maximise press coverage for the company.
Eastern Airways, which operates the route for Flybe, confirmed to The Scotsman it swapped a Loganair plane normally used for the flight for another of the same type of jet with Flybe markings. Eastern said this was so it would be “wholly compliant and in control of the operation”.
The substitution involved an empty Embraer 45 jet being flown some 100 miles from Humberside airport to Norwich to pick up the Royal party and regular passengers.
Loganair’s own Embraer plane then also flew empty some 400 miles from Norwich to Aberdeen so it could operate the next flight back to Norwich.
The Glasgow airline has been subcontracted by Eastern since February for weekday flights on the route.
The source said: “An Eastern Airways jet was flown empty from Humberside to Norwich and then flew the scheduled flight to Aberdeen with the Royals on board.
“The Loganair aircraft which normally flies this route for Flybe and Eastern flew from Aberdeen to Norwich as usual but then flew empty from Norwich to Aberdeen.
“I guess it was to ensure if they had any Press coverage of the Royal travel, an aircraft with a Flybe logo flew them.
“Heck of a carbon footprint to achieve it – not exactly environmentally conscious.”
Royal author Phil Dampier had said: “The contrast between William, Kate and family travelling on a budget flight to Scotland and Harry and Meghan using private jets couldn’t be starker.
“At the very least they know they would have been criticised if they had taken a private jet.”
Flybe said the decision to change the aircraft had been Eastern’s. It declined to comment on the claim that the switch was to gain publicity.
Its spokeswoman said: “We were delighted to welcome the Duke and Duchess of Cambridge and their family on board one of our flights again, this time operated by our franchise partner, Eastern Airways.
“Please note that operational decisions generally are managed exclusively by Eastern on any route they operate under the franchise agreement, hence we are not in the position to comment.”
Eastern Airways said it had chosen to switch the aircraft after being told the Royal party had booked onto the flight.
General manager (commercial and operations) Roger Hage said: “Following a call and details provided late evening on Wednesday as to members of the Royal Family having been booked onto the service, and that armed Royal Protection Officers would accompany the family on-board, we elected, given this service is operated for Flybe by Eastern, to provide our own aircraft and crew, given the approvals and clearance required to accommodate such.
“This then assured ourselves on our own Air Operators Certificate that we would be wholly compliant and in control of the operation in accordance with associated regulation.
“Hence we positioned an aircraft on a short 25-minute leg to facilitate the above.”
An Eastern Airways spokesperson added: “Eastern Airways can confirm any decision as to which aircraft operated the Norwich-Aberdeen service on Thursday morning was entirely that of Eastern Airways and not that of Flybe and apologies to Flybe for any resulting confusion. Decisions taken were to ensure operational control and responsibility remained that directly of Eastern Airways.”
A Loganair spokesman said: “Our aircraft have operated the [Norwich-Aberdeen] route on weekdays since we took on this commitment in February.
“Any comment on tasking requests in relation to the contract is a matter for our customer.”