Opening hours of Japanese banks are usually Monday to Friday from 9pm till 3pm.
To open a Japanese bank account you will be required to produce your Alien Registration Card (all foreigners need this document to legally remain in Japan for more than ninety days).
Note that many cash machines don’t operate during the night and most of them don’t take foreign credit cards. If you want to withdraw money from a machine using your credit card you will have to find an international ATM in a post office, department store, or at the airport.
Here are links to some major Japanese banks with English websites: