Leaving while waiting for business trip visa

A few details about this question.

I'm an American citizen living in Japan for over 9 years with a spouse visa. Started working for a company that requires me to go overseas for business sometimes and next month, mid-May, it will be my first one. I will go to Africa and had to give my company my passport to apply for a visa. The problem is though, I booked a flight to Korea for a few days before Golden week about a month and I'm afraid I might not have my passport.

Is there some kind of permission or, is it possible to get my passport back temporarily? Seems like a strange question I know, and it might not have anything to do with Japanese immigration but, any advice on this will be helpful.

Thank you

You need to ask the company whether it's possible to have your passport back. Alternatively, ask the US Embassy about getting an emergency passport.