It'd take some time explaning the Japanese housing system here. But basically, when you rent a place, you have to pay:

Reservation fee (tetsukekin)
The tetsukekin is paid when you apply for an apartment through a real estate agency, before the actual rental contract is signed. It's a guarantee to you that the apartment will not given to anybody else, and to the agent that you will not change your mind. It is refunded after you sign the lease contract and is usually equivalent to about one month's rent.

Deposit (shikikin)
The deposit is used to cover eventual future damage to the apartment. The deposit minus the cost for repairs is refunded when you move out (in theory). The deposit is usually equivalent to several months' rent.

Key money (reikin)
This is a non-refundable fee to the landlord in the amount of up to several months' rent.

Service fee (chukai tesuryo)
This is a non-refundable fee to the real estate agent in the amount of one month's rent, tops.