A new Lion Air Boeing 737-800 missed the runway and crashed into the sea off Bali in April 13, 2013. All 108 people on board survived, but several were injured.
Indonesia's National Transportation Safety Committee said in its final report on the accident this week that it had identified "a series of errors" by the flight crew.
The captain was unable "to accurately perceive what was going on in the flight deck and outside the aircraft," as stormy weather prevented the crew from seeing the runway, the report said.
"We have conducted an evaluation and taken a series of corrective steps since the accident," Lion Air general director Edward Sirait told dpa.
"We have improved simulation training for different weather scenarios around airports and followed other recommendations made by the regulator," he said.
He also said the carrier had not used the services of the two pilots who flew the crashed aircraft since the accident.
The safety committee released a preliminary report and made several recommendations a month after the accident.
A 48-year-old Indonesian with 15,000 flying hours was the captain while and a 24-year-old Indian national with only 1,200 flying hours was second in command, according to the safety committee's report.
"The pilot in command may have not been aware of the thunderstorm's characteristics, especially the mature state of cumulonimbus," according to the report released this week. "These conditions stated above can be concluded as inadequate situational awareness."
The report said the crew decided to go around and try another approach, when the aircraft was too low for such a manoeuvre. The pilots were also not provided with timely and accurate updates of the rapidly changing weather, the committee said.
Indonesia is facing a shortage of commercial pilots as domestic air traffic grows by about 20% a year and new airlines emerge following the liberalization of the industry in the early 2000s.
Indonesian airlines carried about 70 million passengers last year, amid rising disposable incomes. The number of airliners is set to increase following major orders placed with Boeing and Airbus by Lion Air and state-owned airline Garuda Indonesia.