As I mention in the "Contacting a Japanese Agent Directly" page, if your budget is too low you might need to do the work yourself. But you can try working with any of these companies - it never hurts to try, no matter what your budget is.
Blackship Realty: https://www.blackshiprealty.com/
ehousing: https://e-housing.jp/
Plaza Homes: https://www.realestate-tokyo.com/
Living Japan: https://www.livingjapan.com/
apts.jp: https://apts.jp/