In some places like Kansai International Airport even the space for male and female is separated so everyone can feel comfortable and solemnly pray.
Also there are some prayer equipment such as Qibla direction, veil "mukena" and prayer mat "sajadah" in the female room.
Japan is a great country with a long history. Although so far industrial innovation has been the main focus for Japan, from now on, how to bring the cultural heritage that has been under-recognized in the shadow of history and let the tourists from overseas feel "This is what Japan is about - I want to come again" is the target Japan wants to strive for.
There is a long list of Masjids in Japan on Halal In Japan website which also includes all the existing prayer rooms in the country. The list will be updated regularly.