There is typically 2-4 month’s security deposit (refundable), 1 or 2 month’s key money (non-refundable), 1 month agent fee plus consumption tax (currently 5%), also there may be advance rent that you need to pay upon signing the lease. With properties above JPY 600,000 it is more likely that there will be no key money, but a larger amount of security deposit.
If you are signing an individual lease, having a guarantor could be a must and if you are not able to find one, you may be required to pay 50-100% of 1 month’s rent to an outside company in order to have them act as your guarantor.