At the university, administrators tend to treat people according to how they think their status is (I experienced the same in the USA). If you wear clothes like a student, then there is every chance they will be impolite and impatient. This is nothing to do with you being a foreigner. If you wear a suit then they may be very polite indeed. If your Japanese becomes good enough, there is nothing wrong in putting impolite administrators in their place. Generally though, you should have no trouble. I cannot emphasise enough that patience is a virtue.
Because administrative staff hold the purse strings and other areas of responsibility sensitive to academics, they hold quite a lot of power, and they certainly know it. They are never unfair, but can keep you waiting or be very fussy about the complete correctness of form-filling.
There are ways and means to work around the system, and a lot of this depends on the administrators having the correct piece of paper filled out in the right places. It doesn't matter what is written on the paper, as long as it is completed. Let me give you an example from my own experience as a way of dealing with what may sometimes seem to be bloody-mindedness.
I had been invited to the University of Western Australia to give a seminar. It was during the summer break and I had decided I would go via Singapore to visit friends and also to stay in Perth for about three weeks to talk to some researchers in my field and have a bit of a holiday. I was paying for the whole trip but decided that as there was an `official' aspect then I could apply for formal leave rather than vacation leave. So I duly filled out the leave form in much the same way as I would here with just the minimum of detail. The whole thing was thrown back at me. The clerk in Administration not only wanted to know my complete itinerary of movements in Perth, but wanted to know why I was staying in Singapore for three days on the way. I was more than a little incensed that a young whipper-snapper in the office should poke his nose into my affairs. Naturally, my colleague and good friend Prof Inouye came to the rescue. He said that I must complete the forms properly, and that the clerk was not interested in what was written, just that everything seemed to be properly accounted for in university time, which is what my visit was. So he wrote that the airline connections forced me to make a stopover in Singapore, and what a wonderful opportunity this was to take advantage of their world renowned Singapore University Library. In Perth I was to spend a good deal of time communicating with other researchers in my field and also spend time in the library because of Western Australia's incredible number of endogenous plant species, etc etc. I also had to include the letter of invitation from UWA, which was no problem of course. This was all quite happily accepted. The point is, you must tell them exactly where you will be and what you will do, and it must be seen to be academic; you are not allowed to mix business with pleasure. The one problem with this system is that if you decide to go somewhere else and it is not written on your itinerary held by the university, you'd better not have an accident. If they find out in some way that you are not where you are supposed to be, which they can do from Immigration if you go to another country, then you may lose your job. Its very much like Big Brother and very few Japanese academics like it, but try and argue about it with Monbusho.