The Lion Air plane 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.
Terrified passengers swam to shore or were plucked to safety by police in rubber dinghies. Witnesses and experts have suggested the crash could have been caused by a freak storm, although no official reason has yet been given.
A 70-strong salvage team, made up of military, rescue agency, airport and Lion Air personnel, would remove the seats of the Boeing 737-800 and start cutting up the jet at around 4:00 pm (0800 GMT), military officials told reporters.
"We have two hauling methods, using a crane and floating balloon," said local navy commander Lieutenant Colonel Edi Eka Susanto at Denpasar airport in Bali, where the accident happened.
The parts would be taken to a beach in the Jimbaran area, around five kilometres (three miles) away, he said.
The cockpit voice recorder was found wedged between a wing and the body of the aircraft on Monday, and was being flown to Jakarta on Tuesday, Masruri, from the national transportation safety committee, which is probing the crash, told AFP.
"The black box will be cleaned and checked for damage and hopefully we will be able to extract the data in it," said Masruri, who like many Indonesians goes by one name.
"We will not make any comment on the cause of the crash until we are done studying the data."
Five passengers were still in hospital on Tuesday following the crash, said Lion Air airport service director Daniel Putut, although he said he did not have details of their conditions.
Government officials and the airline said at the time of the crash the weather had been fine.
But the transport ministry has since said the jet was in thick cloud when the accident happened and one passenger has told how the plane was engulfed in torrential rain before the crash.
Indonesia, which relies heavily on air transport to connect its sprawling archipelago of more than 17,000 islands, has one of Asia's worst aviation safety records. The Bali crash was the nation's fourth accident since the start of 2012.