Yes, drinking water from taps in Japan is safe.
For environmental reasons, try to use a refillable water bottle rather than buying bottled water whilst travelling in Japan. Metro train stations have public water fountains, but otherwise these can be hard to find (this is the land of vending machines after all). The best way to guarantee you'll have water when you need it is to fill up your reusable bottle at your accommodation before you leave for the day.
Intrepid is committed to contributing to the preservation of natural and built environments in the destinations we visit, and to reducing the negative impacts our operations may have on the environment. We do this by minimising the use of resources (energy, water, waste) and reducing our carbon emissions in our offices, on our trips and in the destinations we visit. We encourage travellers to minimise their waste by using a refillable bottle. Read more about our responsible travel policy.