burnable gomi For your first 5 years (I believe) you are considered a temporary resident and pay much lower taxes. It'll be less than 10%.
If I'm not mistaken, this is only for careers that are being listed as necessary imports of foreign skills by the Japanese government, like English teachers for example, there are a few more on the list as I recall but aviation professionals is not one of them, you will be taxed without exemptions.
I wish I had better info but Jetstar is structuring their contract different than the others I have seen. Paid in yen, in Japan. The contract agency told me tha the housing allowance or part of it would be exempted from tax but this wont make a huge difference. The tax rates are still very high. I know several ex ANA guys and they said their contract was different.
That is all the info I have.
The contract at SKY for example, they pay your Japanese taxes and your pay is net, you can also use that documentation to lessen or even eliminate your own country's tax liability depending if they do have a non double taxation agreement with Japan or not, or if their rate is higher or not.
The contract at Air Japan is a commuting contract only, therefore you don't have tax liability in Japan because you are not a resident, when they had the 737 contract with ANK, it was also net pay and they took care of the domestic taxes but that contract is no longer available.