For those wishing to visit relatives in Japan or just planning a personal tour without a sponsor, visa applications can no longer be filed directly at the Japan Embassy in Roxas Boulevard. Visa applicants should go through travel agencies duly authorized by the Embassy of Japan in the Philippines. Check their site for the official list of recognized travel agencies.
I went one Monday morning to the Japan Embassy in Pasay to file my tourist visa application only to be told by the security guards to file my papers to one of the accredited travel agencies so I went to the one located in SM Mall of Asia, submitted the required documents, paid Php 2,000 application fee and was told to wait for their call in seven to ten days for the result. When I went back to the travel agency for the result of my application, I was told that my visa application was denied and the processing fee is non-refundable so it was practically gone to waste. HAHAHA! Parang Farmtown lang.
One good thing about this new visa application process is that you can save yourself the burden of having to go through long queues for long hours. The bad is not only you have to pay the processing fee (I never paid anything for my Japan visa in 2004), you also get to doubt the travel agents whether they really tried processing you documents.