Photo booths in Japan are similar to those in Europe but there are some differences.
At first, there are several sizes for ID photos in Japan. Passport requires 4.5 cm x 3.5 cm but 3.0 cm x 2.4 cm is required for driving license. Then, there is a size 4.0 cm x 3.0 cm which is required for ordinary CV and application for Japanese residence card. Therefore you have to choose the proper size carefully before taking the photo at the booth.
Then, there are so many photo booths in Japan. Usually you can find at stations and commercial buildings including convenience stores. Therefore most of the them are reachable 24 hours a day, 7 days a week.
Next, some booths allow you to download the photo to your smartphone. Then, you can use it for online application and also possible to amend the size. To download the photo, you must download the specific application to your smartphone first and then must choose the program which allows you to download the photo. Usually it is expensive than the standard program without download.