It's largely to prevent fraud and money laundering. A significant feature of Japanese bank accounts is money can move between them essentially instantaneously and Japan is a very cash-based society. What banks do not want to happen is for someone to take a cookie-cutter LLC, do an ore-ore fraud (i.e. call up a bunch of Japanese senior citizens and get them to insta-wire their life savings to the new account), immediately convert it into cash ("I need $200k for payroll in $100 bills" is something that is not crazy in Japan -- getting rarer but not crazy), and vanish into the ether. [+]

It does not help matters that a large Tokyo startup was a) a money laundering operation for b) a large international drug network then c) experienced more than half a billion dollars in suspected embezzlement while d) the banking system was caught with it's collective pants down. This current puts a giant blinking Give This Application All Possible Scrutiny on anyone who says "tech company" and "international wire transfer", which is really %#(&)0$ing annoying when you're a tech company which needs to get and make international wire transfers and does not have $100 million of business lying around to justify the bank doing fairly costly due diligence work.

[+] Edited to add: You might not think this sounds like a very plausible fraud, since it requires a corporate officer to make a personal appearance at the bank branch and produce identification, but the corporate officer might be a victim of the scam, too. A "local businessman" who "already owns another corporation so I can't be director of this new venture" approaches them about a great new job as company director, no experience required, the lawyers will take care of everything. The lawyers ("lawyers") draft paperwork and the director stamps everything. On the first day of work the lawyer says "Great. OK, it's the 25th. First order of business: get $200k out of the account at the bank for payroll to the employees at the $FOO branch office. Also, print out a receipt for your own salary; here's the form. We'll meet you at the train station and walk you to the office." At the train station the lawyer looks at the form, notices a misprint, and says "Oh sorry, this is wrong. We don't want to make you look bad on the first day. Tell you what, I'll phone ahead to the company to let them know we're going to be a bit delayed. Wait here, I'll pop back to the office, print the form correctly this time, and we'll go in together then. That's the envelope? Great; give it to me and I'll put it in the safe; wouldn't want someone stealing it at the train station. Society is going to the dogs, you know?"

Later that month, when asked by the police officers, the corporate officer can produce an impressive collection of meaningless powerpoint slides, business cards listing fake names of fake lawyers tied to phones stolen/registered with stolen credit cards/etc, and a total lack of understanding of what went wrong.

Even getting a basic credit card in Japan as a foreigner can be a real pain. If you work for a big company and can get some oomph behind your application you're fine. But if you're a foreign student you're probably going to have trouble.