[konbini]

There are plenty of options but it depends how much you want to spend.

Hotels are quite expensive. Expect to pay at least $150 AUD.
Hostels are cheaper. You can get private rooms for about $50 or share for as little as $25 or $30. In Tokyo I stayed at Tokyo Prince hotel. It is nice place near Shiba park and Tokyo Tower. Asakusa Ryokan Toukaisou is a good hostel in Tokyo. In Kyoto I recommend Hotel Keihan near Kyoto station. However, you might want to stay in a ryokan to get a more traditional feel.