If the plane had hit the flood bank "the outcome for them would have been a lot worse''.
The two men were airlifted to Dunedin Hospital. Both men were outside the aeroplane when emergency services arrived.
Emergency services initially went to the airport, but quickly ascertained the plane had crashed on the other side of the Clutha River, which runs along the end of the runway .
When they arrived at the crash scene, the two occupants were out of the plane, and being assisted by a local farmer.
The instructor was "walking around with a broken arm'' and cuts to his face, and the trainee was lying on the ground, conscious, but with possible spinal injuries that are not believed to be life-threatening.
The pair had flown into Balclutha from Taieri and were attempting a flight to Manderville, near Gore.
Balclutha police, the Balclutha Volunteer Fire Brigade, and St John attended the crash.
The plane would be relocated prior to a Civil Aviation Authority investigation, Snr Sgt Dickie said.