The disruption is affecting some services between Alderney and Southampton, and Alderney and Guernsey.
The airline said the “sole cause of the disruption” between March 21 and 26 is the absence of a pilot at Skybus, which runs services to and from Alderney. Flights are subject to disruption and cancellation.
Philip Saunders, chief commercial officer at Aurigny, said: “As the community would expect, we are working closely with Skybus at this time to ensure that services meet the standards our communities deserve.
“Our dedicated customer services team are on hand to provide all the support you would expect with amending itineraries as required.”
Passengers have been contacted and do not need to contact Aurigny.
Skybus managing director Jonathan Hinkles said: “On behalf of the Skybus team, I would like to apologise unreservedly for the inconvenience caused to the community in Alderney.
“We care deeply about this mission and understand the importance of delivering vital lifeline services to island communities – and we recognise this falls short of what is expected.
“We took immediate steps to advise Aurigny as quickly as possible of our operational capabilities at this time – and to ensure they can support customers with the best alternatives possible.”
Guernsey-based Aurigny Air Services had the second-worst punctuality record for UK departures in 2024, with an average delay of 31 minutes and 12 seconds, according to PA.