Depends on which country will be your residence. You will not have residence in Japan on this contract so you will not have the option to pay Japan taxes. You will have to comply with whatever tax regulations apply to your home country. Your salary is paid tax free so this is your responsibility and in the contract, you agree to release your employer from any tax liabilities. In the US, there are ways to get out of the first 85,000 (somewhere around there), but it is not easy to do. Right now I put aside 30% for taxes and that should cover me until I figure out how it will work.