Check haneda custom website. They actually have a section with Visa.
It says that you should check with your embassy about restrictions and such.
Also I found a PDF from Philippine embassy regarding traveling to japan. regarding to this country passport it says:
- Philippine Passport
• Broken passport is not accepted. Passports must be signed and must have at least two (2) blank visa pages.
Make sure before buying your plane ticket that your trip includes visa for transit. Otherwise this could be problematic.
So if you stay in the transit zone you shouldn't have any visa trouble :)
Hope this helps