The Japanese government has said also that it will do all it can to make sure Asia's largest airline by sales keeps flying.
"The government wants to continue to support JAL to ensure its continued stable and safe operations," Seiji Maehara, the Japanese transport minister, said early on Tuesday ahead of the bankruptcy filing.
Worries over JAL's future have seen its stock price plunge in recent days, losing more than 90 per cent of its value.
By early Tuesday shares in the airline were trading at a record low of just $0.04 as investors jumped ship ahead of the expected bankruptcy.
That left JAL's market value at just $120m, well below the price of just one new Boeing 787 jet.
"The new DPJ government has publicly said that it would tackle the issue of JAL's continuing problems head on and that's what it's done.
"The government providing $3.3bn of emergency funding immediately.
"Emergency loans being made available of up to $6.6bn and that's on top of vast lines of credit that the government had been providing just to keep it running."
Following the bankruptcy proceedings, the restructuring of the airline will be led by a new chief executive – Kazuo Inamori, one of Japan's richest entrepreneurs.
Inamori founded the Kyocera electronics group, as well as Japan's number two mobile phone network, KDDI.
However, he has no experience in the airline industry.
The restructuring plan calls for about 15,600 job cuts, or a third of JAL's workforce, and will require the airline to halve the number of its subsidiaries which span everything from hotels to credit cards.
In turn the government-backed Enterprise Turnaround Initiative Corp will invest about $3.3bn in the carrier, while JAL's main lenders have been asked to write off about $3.8bn in liabilities.
Despite JAL's financial woes, however, the airline remains a prized asset for foreign airlines because of its extensive access to Asian routes.
Recently the Skyteam airline alliance led by Delta airlines has been involved in a fierce tug-of-war trying to woo JAL away from its current membership in the One World group, led by American Airlines and British Airways.
Delta and its Skyteam partners have offered $1bn, including $500m in cash, to lure JAL away from One World.
At the same time American and its partners say they are ready to inject $1.4bn in cash into the Japanese airline, up from a previous $1.1bn offer.