The incident at the Moray air base involved a SAAB-Scania cargo plane with two crew on board on 8 October 2008.
The pilot tried to brake hard after spotting two deer run in front of the aircraft on the runway.
His actions caused the plane to veer left causing one of the animals to hit the propeller and damage the fuselage.
The impact brought the plane to a halt.
None of the crew were injured.
The AAIB report did not reveal the fate of the two deer.
The accident report said that incident happened following an "uneventful" flight from Edinburgh.
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