The NTSB reported the captain (48, ATPL, 15,000 hours total, 7,000 hours on type) was pilot monitoring, the first officer (24, CPL, 1,200 hours total, 923 hours on type) was pilot flying.
The aircraft positioned for the VOR/DME approach to runway 09 with MDA at 465 feet AGL (editorial note: the chart by AIP Indonesia identifies MDA at 465 feet MSL and 454 feet AGL). While descending through 1600 feet the aircraft was cleared to land on runway 09 by Tower who reported winds from 120 degrees at 5 knots.
According to the flight data and cockpit voice recorders the aircraft was descending through 900 feet AGL when the first officer stated the runway was not in sight.
37 seconds later the aircraft descended through 550 feet AGL, the EGPWS called "MINIMUMS", the autopilot and autothrottle were disconnected and the descent was continued.
At about 150 feet AGL the captain took over control of the aircraft, the first officer acknowledged and stated he could not see the runway. 8 seconds later the EGPWS called out "TWENTY", the captain commanded "Go Around", one second later the aircraft contacted the water surface, the flight data recorder recorded the last position of the aircraft, likely the point of impact, at S8.7503 E115.1503, the aircraft was configured for landing with gear down and flaps at 40 degrees. The aircraft came to rest facing north about 300 meters southwest of the runway threshold.
Two aircraft were holding at holding point runway 09, one of the pilots called tower reporting the LionAir had just crashed into the sea. The tower controller could see the tail section of the aircraft in the water and pressed the crash button to alert emergency services.
Water entered the aircraft from the aft cabin, most passengers evacuated via the overwing right hand emergency exits and right hand forward door which were the doors nearest to the shore, the flight attendant opened the forward left hand door and inflated the slide with the help of a passenger, several passengers jumped into the water and swam ashore, others were assisted by rescue boats. 45 minutes after impact the evacuation of the aircraft was completed, the injured occupants had been taken to hospitals and the others collected at the airport crisis center.
5 minutes after the aircraft contacted water first emergency services arrived at the scene and began rescue operations.
Four passengers received serious injuries, 97 passengers and 7 crew received minor or no injuries. The aircraft was substantially damaged.
The crew of another aircraft 5nm behind PK-LKS reported they could not see the runway at minimums and went around, on their second approach they could see the runway before minimums.
One of the crews at holding point 09 reported that there was rain and visibility was about 1-2km, when the Lionair was on a 3nm final he could not see the aircraft except on TCAS display.
The NTSC reported that surveillance cameras at the south side of the runway showed the weather was changing, there was rain in the left hand corner of the image, the final approach however was clear 4 minutes prior to the accident and there was rain in the final area a few seconds prior to the accident.
The NTSC reported the VOR and DME were both working properly, PAPIs and runway lighting were working properly at the time of the accident.
The NTSC stated in their first findings, that the short final was outside the envelope of the EGPWS warning, hence no EGPWS alarms were recorded.