The LM901 flight landed back at Aberdeen safely at about 8.15am.
Loganair confirmed that the crew on-board made the decision to turn back due to an “alert of a fault” with the right-hand engine.
A spokeswoman added: “The passengers will resume their journey on a replacement Loganair aircraft this morning, and engineering checks to identify the cause of the warning indication are already underway.
“We apologise to customers for the disruption to their journey, yet ask for their understanding that safety is always our first priority.”
Aberdeen International airport has been approached for comment.
Flight from Aberdeen to Shetland declares emergency mid-air due to engine fault