The pilot of the Piper Cherokee aircraft had to decide quickly whether to carry on with the landing on a grass runway at Full Sutton Airfield in Yorkshire, the Air Accidents Investigation Branch (AAIB) report said.
The aircraft overran the runway, went onto unprepared ground and overturned.
The pilot and two passengers were able to get out but one of the passengers suffered a serious injury.
Describing the incident on the early afternoon of October 20 2014, the AAIB said the pilot had noticed the flock of birds on the runway but she thought they would disperse as the aircraft got nearer.
With the aircraft descending to about 100-150ft, the birds rose from the runway and into the aircraft’s path.
The aircraft, flying from Wellesbourne Mountford Airfield in the West Midlands, struck at least two birds, with one hitting the propeller, leaving remains on the windscreen on the passenger side.
The report went on: “The relatively inexperienced pilot was faced with a critical situation just before landing and had to decide quickly between continuing to a landing some way up the runway or to go-around and make a further approach with the full landing distance available.
“Uncertainty over the aircraft’s condition and the probably shock factor of an unexpected and unpleasant event would have been factors in the pilot’s decision to continue the approach.”