The Eastern Airways flight bound for Sumburgh in Shetland returned to Aberdeen around half an hour after squawking the 7700 code which tells air traffic control that it has a problem.
A spokeswoman for the firm said that the captain had been forced to shut down an engine after a warning light went on.
The flight, T3105, issued the alert at around 10.20am. The same flight, which today used a a BAE Jetstream 41 plane, had to make an emergency landing at Aberdeen in February after apparent problems with its landing gear.
A spokeswoman for Eastern Airways said: “Shortly after departing from Aberdeen for Sumburgh, charter flight EZE1035 returned to Aberdeen due to a warning indication relating to one of the aircraft’s two engines. As a precautionary measure, the captain decided to shut down the affected engine following a bird strike.
“The Jetstream 41 aircraft with 17 passengers and three crew on board landed safely at Aberdeen at 1045. Passengers disembarked the aircraft as normal via the aircraft steps. Engineers are inspecting the aircraft."
She added: “We apologise to passengers for the inconvenience, but the safety of our passengers and crew is our number one priority.”
Last year, Eastern Airways teamed up with FlyBe Eastern to operate flights for the airline between Sumburgh and Edinburgh, Glasgow and Aberdeen, although this flight was believed to be a private charter. It also flies between Stornoway in Lewis and Glasgow, and between Kirkwall in Orkney and Aberdeen.