From my experience in the Tokyo area, the cleaning/restoration fee is negotiable if:
-you haven't put money down
-The contract doesn't stipulate it directly
-you're willing to play hardball
At our last place, we just cleaned the apartment ourselves after moving out. While moving out, we found some serious water damage underneath a bookcase that hadn't been moved for two years (probably due to the wood flooring having been installed directly on the concrete). He quoted us a price to fix it and we talked it over. My SO said we didn't really have to pay any of it, but it's usual to pay about half of what they quote. Of course, this could mean they just pre-inflate their prices by 2x.
At our last place, we just cleaned the apartment ourselves after moving out. While moving out, we found some serious water damage underneath a bookcase that hadn't been moved for two years (probably due to the wood flooring having been installed directly on the concrete). He quoted us a price to fix it and we talked it over. My SO said we didn't really have to pay any of it, but it's usual to pay about half of what they quote. Of course, this could mean they just pre-inflate their prices by 2x.