Commander Capt Z Glusica and co-pilot H S Ahluwalia informed the Air Traffic Control that the aircraft was established on the Instrument Landing System approach at about 10 miles from touchdown.
The ATC gave the pilots clearance for landing when the aircraft was about four miles from touchdown, an Airport Authority of India official said.
The wind was calm, visibility at a comfortable six km and it was not raining at the time of the incident.
The pilots reported no problem as they prepared to land at Mangalore in the small hours of the morning.
But the wheels of the Boeing 737-800, with 166 people on board, touched the ground slightly beyond the touchdown zone on runway 24.
As a result of this, the aircraft overshot the runway, and went beyond the 90 metres of the runway end safety area and straight into the valley.
The Mangalore airport is a licensed airport with a runway length of 2450 metres (approx 8000 feet). It also has a runway end safety area of 90 metres.
The runway was commissioned in 2006 and has remained operational since then.