Until you actually sign for a place there’s no charge for using an agency however. Be aware of the substantial move-in fees that a new flat in Tokyo will normally incur, such as your first month’s rent, a two to three-month deposit (make sure you get a written receipt for this), key money (non-refundable and can sometimes be as much as two-months’ rent!). If you do decide to go through an agency take your time to look at lots of places since the first ones they show you may be the properties they’re anxious to rent but may not be the best for you.
Try to hold out until you find something that’s really suitable. Since move-in expenses are high don’t rush into signing anything until you’re really satisfied. Japanese apartments tend to be small so have a good look at storage space and the bathroom.
If you get a Japanese person to help you deal with the landlord and/or agency it will be a big help. The following links are for agencies where English is spoken: