Essentially the visa is free of charge but you need to pay a fee to the travel agency that will process the visa for you. Note, you cannot go directly to the Japan embassy. You must process your visa via one of their accredited agencies.
Fees will range between P500-P2,500 depending on the agency. 500 peso application only happens during travel expos, and note that a higher fee doesn't mean higher chance of visa approval.
I got mine at Reli Travel and Tours in Megamall and paid P1,000. I processed mine with them due to proximity to our house, plus my Dad and other relatives used them in previous travels with no problems.
Things you ought to prepare before applying for visa:
1. Make sure your passport is not expiring within the next 6 months counting from your travel date to Japan. I know this is a stupid rule, but friends of mine got left on a Singapore trip because of this really stupid policy.
