The 43-year-old man was moments from lift-off at East Fortune Airfield near North Berwick in East Lothian when several sheep jumped over a fence from their enclosed field and crossed the runway ahead of him.
He aborted the take-off and hit the brakes, managing to pass through the middle of the flock without hitting any.
As the runway was coming to an end, he turned off the engine and the microlight crashed into a concrete roof truss that had been placed across the runway's end.
The accident on September 28 last year was reported to the Air Accidents Investigation Branch (AAIB) by the pilot and details were published in its latest bulletin.
It said the weather was good in the area and another pilot had made a successful take-off just two minutes before the accident.
The report said the landowner around the airfield has now decided not to keep sheep near the runway and will graze other livestock in enclosed areas nearby.
The aircraft involved was a Mainair Blade 912 with only the pilot onboard. The crash caused damage to the landing gear and main body of the aircraft.
The AAIB report said: "As his take-off progressed, one sheep, followed by several more, jumped an adjacent fence and crossed the runway ahead of him.
"Although he had been just about to rotate, he aborted the take-off, reducing power to idle and braking.
"The aircraft passed through the middle of the sheep, just missing them.
"The pilot realised that there was insufficient runway ahead in which to stop, so switched off the engine. The aircraft impacted a concrete roof truss which had been placed across the runway's end.
"The pilot vacated the aircraft without difficulty, having suffered only minor injuries."