INDONESIAN investigators have begun retrieving the wreck of a Lion Air plane that crashed at Bali's airport, as accounts emerged of a freak storm that could have caused the accident.

The Boeing 737-800 missed the runway as it came in to land on Saturday, slamming into the sea and splitting in two.

Dozens of the 108 people on board were injured, but there were no fatalities.

After the plane hit the water, terrified passengers swam to shore as police came to their aid in rubber dinghies.

Government officials and the airline said at the time of the crash that the weather had been fine.

But on Monday, transport ministry official Herry Bakti said the plane had been travelling through dense cloud at the time of the incident and one passenger told how the aircraft became engulfed in torrential rain.

French businessman Jean Grandy, 49, one of four foreigners on the plane, said that the flight from the city of Bandung in West Java had appeared to be landing smoothly.

"The final approach was fine," he said.

"Then suddenly, a cloud enveloped us. Torrents of water were pouring on us, it was an enormous downpour. It only lasted two, three minutes.

"It was almost as if it was night, even though the sun had been shining just before," said Grandy.

The Frenchman, who owns a shoe factory in Indonesia and lives in Bali, said it was an "extraordinary phenomenon" that could have happened to any plane - and that he planned to fly on Lion Air again on Wednesday.

His testimony supported the views of some analysts who said that as the plane was new, a freak weather incident may have caused the crash of the Boeing 737-800, which was delivered to Lion Air only last month.

Tom Ballantyne, chief correspondent of Orient Aviation magazine, said the accident could have been caused by a change in wind direction and speed between different altitudes, or a strong downdraft from storm clouds.

"If that hit the aircraft when it was on final approach, there is the likelihood the pilots would not have had time to recover," he said.

The Indonesian pilot, Mahlup Gozali, who had more than 10,000 flying hours, and the Indian co-pilot, Chiraq Carla, tested negative for drugs and alcohol in preliminary tests, a transport ministry spokesman said.

Divers on Monday retrieved the cockpit voice recorder, which had become wedged between the body and wing of the wrecked plane, and pulled other small debris out of the water.

Salvage teams will be lifting the body of the plane in three parts, said Bali airport general manager Purwanto.

The tail will be lifted using a crane on Monday evening, and the whole operation should take two to three days to complete, said Purwanto, who like many Indonesians goes by one name.

Transport ministry official Bakti said that an interim report should be complete in around a month, but could not say when a final report would be completed.

Launched 13 years ago with just one plane, Lion Air has struck two of the world's largest aircraft orders in a staggering $US46 billion ($A44.00 billion) bet on Indonesia's air transport boom.

Saturday's crash has heightened fears the plans are overambitious for an airline that already has a poor reputation, has suffered a string of accidents, and is banned from EU and US skies because of safety fears.