Parts of the propeller were smashed off as the SAAB-Scania aircraft moved along the air base runway at nearly 60mph.
Air accident investigators revealed how the 33 year-old pilot tried to brake hard but failed to avoid the wild animals.
They struck the propeller and damaged the fuselage, bringing the plane to a halt.
The pilot and his colleague were the only people onboard the 2am flight from Edinburgh on 8 October last year.
They were uninjured, but the fate of the deer is unknown.
An Air Accidents Investigation Branch (AAIB) report said the crash followed an “uneventful” early morning flight north from Edinburgh.
It stated: “At about 40 to 50 knots during the ground roll, two deer were seen to run in front of the aircraft from left to right, a short distance ahead.
“The commander applied maximum braking and steered the aircraft to the left as far as he was able without risking a loss of directional control.
“The deer passed down the right side of the fuselage and struck the right hand propeller.
“The crew brought the aircraft to a stop and, with vibration from the right engine apparent, both engines were shut down.
“Upon inspection, a propeller tip was found to have sheared off and made contact with the fuselage side.”