The 43-year-old man was moments from lift-off at East Fortune Airfield near North Berwick, East Lothian, when the sheep jumped over a fence 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 the sheep. As the runway was coming to an end, he turned off the engine and the microlight crashed into a concrete roof truss across the runway's end.
The accident on September 28 last year was reported to the Air Accidents Investigation Branch 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 had now decided not to keep sheep near the runway.
It said: "As his take-off progressed, one sheep, followed by several more, jumped an adjacent fence and crossed the runway ahead of him. He aborted the take-off. 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 suffered only minor injuries.