I'm arriving at Narita airport at 9:30 pm, and departing from Haneda airport at 9:30 am the following day. I am a Filipino citizen working in The Bahamas.
Will I still need a transit visa?
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The simple answer is that you'll need a visa.
You are arriving in one airport and then departing from another, so you'll need to enter the country to get between them. This means that you either need to be from a country that does not require a visa for Japan (which doesn't include the Philippines), or have some form of pre-arranged visa.
Technically Japan does have a concept of a "Shore Pass" (sometimes called a "Transit Pass") that can be used in situations like this, but in general it's not possible to use it. The Shore Pass needs to be requested by the "captain" of your "ship", which basically means that the Airline needs to request it on your behalf - you can't do it yourself, and as a rule airlines will not do it for you.
Even if you could talk the immigration officials in Narita into giving you a Shore Pass it still not going to be possible, as the airline will not let board the flight to Japan without the proper documentation.
Note that even if you can change your flights so that they are both to/from the same airport then you may still need a visa. Japan does allow "Transit Without Visa" (TWOV) as long as you stay airside (ie, don't pass through immigration), however in Narita this is only allowed if you are departing on the same calendar day as you arrive - an overnight stay still requires a visa. Haneda on the other hand will allow you to stay for up to 72 hours in transit (because what could be more fun than spending 3 days airside in an airport!)
As stated by Timatic, the database used by airlines:
Holders of onward tickets transiting to a third country can obtain a Shore Pass on arrival for a max. stay of 72 hours only if there are no connecting flights on the same calendar day
So, despite the other answer stating otherwise, this is a very real option. Present your passport and connecting boarding pass (or e-ticket, if you can't print the boarding pass in advance) to immigration at Narita.
One requirement is:
Departing from the same airport of arrival, or from a different airport (or seaport) around the airport (or seaport) of arrival, if both ports are located within the same group below:
Group A: Airports: Narita (NRT), Haneda (HND), Nagoya (NGO), Niigata (KIJ), Komatsu (KMQ) and Yokota.
So no, you do not need a visa