Upvote:-3
I do not think the embassy in Philippines can really help you because the immigration is another department. Although you have a visa from the embassy, the immigration still can reject you without any reason given. But you need not worry because there is a nice hotel in the airport before the immigration. So what I mean is the only people who really knows are the immigration in Narita. From what I know as a hyper frequent traveler, the officials in Narita will help you but your luggages may give you problems.
Upvote:1
Where did you get issued the "single ticket"? Neither Air Philippines nor Air Tahiti Nui fly that route (as far as I could find). Did you purchase these tickets on flight aggregation sites which has essentially given you two separate tickets?
In Narita Airport, there is a transit path that allows you to transfer from one flight to another without going through immigration. Unfortunately you will be unlikely to use this if you need to collect your baggage, which is after immigration. See the connections guide on the Narita Airport page.
If your luggage is not tagged to your final destination, you will need to go through immigration then collect your luggage, then check in again in Narita. As you are a Phillipine National, you will need to contact the Embassy of Japan for a transit visa.