We, with a Philippine passport may not have been given the no-visa privilege when entering Japan (for now), a free visa fee and some leniency (compared to how it was couple of years back based on some friends accounts) are enough for now to secure a pass to probably see Mt Fuji up close and personal.
Please note that this is my personal visa application experience - for tourism purposes only and personally-funded. Other visit visa types would require a different set and/or additional documents.
Actual lodging of application at the Japanese Embassy here in the Philippines should be done thru an accredited travel agency. I sought Friendship Manila's service for a fair price of Php1200 single entry. They will be able to provide additional information too as to the other visa types.