No, it can’t. Just passing through the Philippines sea zone counts as two movements (one in, one out), since the fighter doesn’t actually enter the island territory. However, attacking the Philippines territory would cost two extra movements: one to enter the Philippines from the sea zone and another to exit the Philippines back into the sea zone.
Your example would look like this:
1. Japan to sea zone 62.
2. Sea zone 62 to sea zone 60.
3. Sea zone 60 to sea zone 50.
4. Sea zone 50 to Philippine Islands.
5. Philippine Islands to sea zone 50.
6. Sea zone 50 to sea zone 49 (carrier).
As you can see, a standard fighter would be out of movement at the Philippines, with nowhere to land, making this an illegal move.
However, if the same fighter took off from a carrier in the Japan sea zone, it could attack the Philippines and land on a carrier (perhaps the same one) in the Philippines sea zone:
Sea zone 62 (carrier) to sea zone 60.
Sea zone 60 to sea zone 50.
Sea zone 50 to Philippine Islands.
Philippine Islands to sea zone 50 (carrier).
Each time a plane crosses a boundary between spaces (whether between land or sea or both), it uses one movement point.