For rental housing in Japan, lease contracts are renewed every two years. This is called keiyaku koshin (contract renewal). When you want to renew the contract, you need to go to the real-estate agent and submit renewal fees and other items as requested.
On the other hand, if you want to terminate the contract for leaving Japan or moving to other places, you need to notify the real-estate agent and the landlord, at least one or two months in advance.

When you want to renew the contract, you need to apply to the real-estate agent and the landlord. In many cases, rents are raised upon renewal and the landlord may ask for a renewal fee (equivalent to one month’s worth of the new rent). You may be also charged renewal fee from the real-estate agent.
For the renewed contract, in most cases the same document signed in the previous contract will be carried over. Sometimes the real-estate agent contacts you before expiration to ask whether you want the renewal. Also, there are cases that rents are not raised and renewal fees are not charged from either landlord or real-estate agent.

When you want to terminate the contract, you need to notify the landlord either directly or through the real-estate agent of the intention to move out. It is important that you make an early notice. As may be stipulated in the contract, you must notify at least one or two months in advance.
If you move out without notifying the landlord or notify just few days before moving out, you may not get the deposits back. So be sure not to postpone termination notice.