The incident at Durham Tees Valley Airport led to emergency services being scrambled, although none of the three people on board the Falcon 20 were injured.
It was operated by Cobham Aviation Services, an international firm whose activities include training military personnel.
A spokesman for the firm said: "An aircraft operated by Cobham Aviation Services was involved in an incident at Durham Tees Valley Airport.
"A bird strike was reported resulting in an aborted take-off and the aircraft overran the end of the runway. The three crew on board were uninjured and the aircraft has sustained some damage.
"Cobham Aviation Services has launched an internal investigation into the incident and are fully co-operating with the airport and with the Air Accident Investigation Branch (AAIB) who will also conduct an investigation."
Bird strikes are frequently the cause of air accidents and are particularly dangerous if the bird is sucked into a jet's engine.
The airport, near Darlington, continued to operate as normal after the incident, said a spokesman.