Via The Japanese Ministry of Foreign Affairs: the Japanese government has substantially relaxed visa requirements for travelers from the Philippines, Vietnam, and Indonesia.
Multiple-entry visa requirements have been substantially relaxed, and requirements for single-entry tourism visas will be relaxed to a quasi-exemption-equivalent level when applied via specified travel agencies.
The quasi-exemption-equivalent level is similar to South Korea visas for Filipinos, wherein you are technically free to come and go, however you are still required to apply for a visa as a formality.
Currently, Philippine passport holders traveling to Japan on short-term visits of up to fifteen days are qualified to apply for multiple entry visas with three years validity. Complete instructions for applying for a multiple-entry visa can be found here.