Lockers and Baggage
It's inconvenient to explore a city with a rucksack aback, so lockers are a nice and inexpensive solution. The Japanese usually travel by train, so most stations, airports and bus stops have coin lockers.
Large (all Shinkansen "bullet train" stations), most medium-sized and many small stations in popular tourist areas have coin lockers. Information centers there may also offer some locker space. Many stations have diagrams in English helping tourists locate lockers. You can also leave your stuff with station personnel - ask someone at an info desk or at the ticket gate - at a restaurant or hotel nearby.
Costs
Basic costs are generally 300 yen (small), 400 yen (medium) or 500 yen (large) for each calendar day. So leaving a bag overnight in a small locker costs 600 yen. The maximum period to check bags for is 3 days. Station employees remove bags left longer and hold them generally at the Lost Baggage.
Station Hours
There is little night train service in Japan, so most stations or some large station areas are closed between late evening (11 pm - 1 am) and early morning (around 5 am). English signs for locating lockers, hours of use, and coin instructions etc. are widespread. You can also locate station personnel by their uniform and ask them for assistance.
Airport Coin Lockers
All the major airports - Narita (Tokyo), Kansai (Kyoto and Osaka) and Centrair (Nagoya) - offer coin lockers and baggage shipping services (takuhaibin) to send bags anywhere in the country at reasonable cost and time. Coin lockers are also available at smaller airports such as Fukuoka or Chitose (Sapporo).
Lost Baggage
In Japan your baggage is likelier to be forgotten by yourself than stolen. Then you should contact the Lost Luggage office (in Japanese: o-wasuremono azukari-jo). Larger stations are located separately, at smaller ones you can go to the stationmaster's office (ekicho-shitsu).