It would be helpful if you told us which airline(s) you are flying, which Japanese city you are passing through, and which airports you will be using.
Tokyo has Narita and Haneda airports, each with three terminals. These are some of the best and most efficient airports in the world. If your flights are connecting in the same terminal, you may need only an hour or so between flights. If you are commuting between terminals, it could take much longer. If you must commute between the two airports, it will take you far longer.
If you are flying through KIX Airport in Osaka, nearly the same story.
Generally you can trust the airlines to know how long it will take you to make a connecting flight. They do not want pax missing connections and stuck in airports, needing yet another flight. When you book your flights, they can advisse you on the approximate connecting times.