You first should ask the company the reason why they need your passport. You can refuse in general, while the company needs your passport to get your permission from the immigration authorities. If you can go to the immigration office by yourself, you do not need to give your passport to the company. When a foreign resident in Japan wishes to change status or extend the period of legal stay in Japan, the passports should be shown at the immigration service bureau at the time of both the application and the permission. Lawyers or company personnel who is registered at the immigration offices are able to act on behalf of the foreign applicant by submitting the documents, including a passport.
Am I required to turn in my passport as a work visa holder if my company asks?
As a skilled worker from Indonesia, I just obtained a work visa and start a new position in a company based in Japan. My employer is asking me to hand in my passport. Is this a legal requirement? Can I refuse to do so?