Japanese companies share the characteristics of Japan as a whole, with seniority being taken very seriously, personal responsibility being required of members, and there being forms and paperwork for everything imaginable.
Here are a few tips for working in a Japanese company gathered from those who have been in that environment for several years.
1. Do lots of behind-the-scenes networking
Coming in at 9, doing your work and leaving at 5 (or 6, or 7, or 8!) will ruffle no feathers, but won't necessarily get you far ahead. The way to get ahead in a Japanese company is to make yourself useful to as many people in the organization as possible. This requires getting on side with people on a personal basis. Just because you're in the same company doesn't mean at all that people will feel free to approach you with requests.
As in Japanese society at large, in general, the only Japanese people who take the initiative when dealing with a foreigner are those who are those in authority, those who are exuberantly confident (often to the point of being pushy), those who are desperate, or those who are nutty. It is therefore in your interests to take the initiative (within the bounds of seniority) and choose whom you want to have something to do with by approaching likely looking people in your company and selling yourself. A very important part of this is socializing - typically by going out for lunch together. The more people you can create relationships with, and work together with - without overstretching yourself, of course - the better your chances of promotion, whether within the company, or by changing companies thanks to connections who have moved on to other things. The literal meaning of the word "company" is especially important in Japan: ultimately it's as much about the people as the work.
2. Take responsibility and be self-reliant
Seniority in Japan is strictly adhered to (as dealt with below), but don't expect your boss to be your mother hen. Japanese companies are often not particularly rational or efficient when it comes to communication channels. There are emails every day from all sorts of different people and departments that have to be gone through very carefully. If a meeting is to take place at 3pm, and will be attended by all those around you, don't expect anyone to remind you about it. You'll raise your head from your computer screen to find all the seats around you empty. Everyone has gone to the meeting without the boss giving any verbal reminders or without any of your colleagues having said anything either. It's just the emails and your clock and you. And having been engrossed in work is no excuse for absence or lateness. And not having been bothered to read those three pages of instructions about how to fill in the new (poorly designed, overly complex, unintuitive) time-chargeability sheet is no excuse for getting it wrong. It's very much a matter of entrusting you with the big things only when you've proved trustworthy regarding the little things.
3. Respect seniority and others' sense of pride
While respecting seniority is important in companies all around the world, in Japan (and Korea) in particular, deference must be paid even to those in more senior positions outside of your department, even if they just started their job yesterday. This extends to little things like letting them through a door first, and of course to the bigger things like letting them have their say in things that matter, and - very importantly - using the correct language and manner when speaking to them.
Pride in Japan tends to be very brittle, so keep in mind that any behavior seen as overweening is keenly resented. This goes even for apparently innocent things like, maybe, showing a colleague a simple keyboard shortcut to make his or her workflow more efficient. Unless you are officially that colleague's boss, or unless you have a very close relationship of trust, don't even bother.
Everything else, like being honest and conscientious, being flexible, being personable and engaging, being efficient, being forgiving, etc., are qualities that will get you as liked and needed in a Japanese company as in a company anywhere else. But networking, being self-reliant and responsible, and being respectful of others in the context of the seniority system will be especially fruitful when working in a Japanese company.
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