How/when to pay taxes on income outside Japan

So my employer pays me bonus in form of stocks into an overseas bank account. I am pretty positive that I have to pay taxes on them too, since they are an income as well. But I haven't seen any way yet to pay them. Does anyone have experience on how that works? It might also be worth mentioning that 2016 was my first year of working in Japan. Would love to hear your experience.

Issue of stock (shares) isn't into a bank account. Seems like a muddle of terms - can you be clearer? Did you get company stock or cash? If stock, what is the current redeemable value? They would be the starting points.

The bonus is in form of company shares, yes. The value is around 9000 UD. If it matters: I am not a permanent resident (instead 5 years work visa).

if you really got your company stock by no payment, it will be considered as a salary.
(getting the company stock is that your name was registered as the stock holder.)