Yes. Some things can be negotiated, but the truth is that negotiations generally only become viable when rent exceeds ¥350,000/month or so. Lower rent priced units are so in demand, that property managers have no reason to negotiate terms, as someone else will take the unit very quickly with no issues.
Please note that negotiations are difficult if the listing is a popular property or if you are looking to move during a busy season. Also, please keep in mind that although applications to apartments are on a first-come-first-served basis, landlords may choose the second applicant if they provide a better offer. Please consult with us on how best to approach a deal, as negotiations can only happen at the time of applying (this shows that the potential tenant is serious).