I studied in Japan for a year in 2000-2001. My case may have been different because I got a scholarship from the Japanese ministery of education.
A few days after arriving, us international students were taken to a local bank (or maybe a bank employee came to the university, I don't remember) to open accounts to which the scholarship would be paid. This was a routine procedure, and there were no problems. However, it took almost two months for the first scholarship sum to arrive, and we had been advised to bring enough money of our own to last this time. I think I just took cash.
So the first thing you might do is to ask the Japanese university's foreign student department about bank accounts.
As for using international banks (specifically Citibank) to transfer money, this was in fact the recommended procedure back then, since most Japanese banks will not accept foreign cards in their ATMs at all, nevermind fees. The biggest exception is the post office, which does accept debit cards on the Maestro network (at least it did when I returned to Japan in 2005).
As for fees, you have to be aware that they are mainly set by your own bank that issued the card: credit cards companies typically ask percentage fees that can get very expensive on larger sums, but at least here in Germany, bank-issued Maestro debit cards carry only a moderate flat fee of 4.5 EUR per international cash withdrawal. So it might be a good idea to compare Russian banks in this regard.