Employer surprised me with 100,000 yen bill I "owe" for my visa

First and foremost, it is illegal for them to deduct those funds from your salary without your permission.

It is highly unusual to attempt to recoup expenses involving visa processing from employees, and even more so to do so without prior agreement regarding the amounts paid. The basic rule is that if they spend the money without an agreement in place, it's on them. It smells like your local manager messed up the process and exceeded their permitted spend, and are trying to avoid having to explain the extra expense to their own boss.

You can go over this with the labour bureau beforehand without actually requesting action just so that you can be sure you have the correct information. If they are in fact pushing this issue, though, it's an excellent sign that you will want to find a new job ASAP.

/r/japanlife Thread