Hi!
In most Japanese residential rental agreements I've seen, there is a section where the real estate agency (宅地建物取引業者) and the real state agent (宅地建物取引士) put their stamp (jitsuin) on it as a sign of validation.
Just thinking about real estate in general there are often two parties to a transaction, one representing the buyer and one representing the seller, and they each want their fee. That would be my guess.
I agree with @mdchachi. It's probably not uncommon to have two real-estate agents involved, one for the seller/landlord/lessor and the other for the buyer/tenant/lessee.