Around 4-5 hours!

You have not mentioned the destination city in Japan so I will give you some information about some of the cities:

- Tokyo: The distance between Manila, Philippines and Tokyo, Japan is 1867 kilometers or 3004 miles. A direct flight will be 4 hours and 25 minutes long and link flights may take up to 18 hours and 30 minutes.
- Osaka: The direct flight from manila to Osaka is 3 hours 50 minutes while link flights can take as long as 20 hours and 15 minutes.
- Hiroshima: The direct flight from Manila to Hiroshima is 9 hours and 55 minutes and a link flight can take as long as 23 hours and 20 minutes.
- Nagoya: The direct flight from Manila to Nagoya is 3 hours 55 minutes long while it can take up to 29 hours and 45 minutes if its linked.