About 45 injured people were taken to hospitals for treatment, but there were no serious injuries, according to an airport spokesperson.
TV footage showed rescuers using rubber boats to evacuate the 101 passengers and seven crew members. The Boeing 737 could be seen sitting in the shallow water with a large crack in its fuselage.
Authorities initially said the plane overshot the runway before it hit the water, but a Lion Air spokesman said at a news conference that the plane crashed about 164 feet ahead of the runway. The weather was cloudy with rain at the time of the incident.
Spokesman Edward Sirait said the jet failed to reach the runway and fell into the sea. He said the Boeing 737-800 Next Generation plane was received by the airline last month and was declared airworthy.
Strait said the airliner has not pinpointed the cause of the crash yet, adding that the National Safety Transportation Committee was investigating.
Lion Air is currently banned from flying to Europe due to broader safety lapses in the Indonesian airline industry that have long plagued the country. Last year, a Sukhoi Superjet-100 slammed into a volcano during a demonstration flight, killing all 45 people on board.
The Associated Press contributed to this report.