Flights on Friday and possibly Sunday to and from Alderney are impacted. Customers will be offered a full refund or an alternative journey on boats that the airline has chartered.
For Dornier flights to run safely and operate in accordance with regulations, a First Officer and a Captain are needed.
Aurigny said a catalogue of events has left it with a shortage of First Officers.
Crew in quarantine following period of essential training overseas (in Germany)
Unexpected resignation of a First Officer
Unable to use UK contractors due to quarantine restrictions
Delays in training of newly recruited pilots due to Covid – because of restrictions on access to European simulators
Pilots flying the maximum permitted hours
Also, one of its crew has been signed off sick this week.
Mark Darby, chief executive said: ‘The crew operating the Alderney route have been busier than ever this summer and I would like to personally thank them all for their hard work.
'It is hugely regrettable for Aurigny that this is happening on the last Bank Holiday of the summer when many people had booked Staycations in Alderney and Guernsey.
'We are doing everything we can to help make alternative arrangements for all of our customers.’