Also known as pit toilet or squat toilet. Pit toilets are not only found in Japan, or in Asia (I first used modern pit toilets in Senegal), but the modern pit toilet is often referred to a Japanese toilet even when found in America or Europe. I assume this is because more Americans travel to Japan on business than to Africa.
These are toilets that are set into the floor, so that the top of the toilet is at floor level. You squat over them, so that your bottom does not touch any part of the toilet. These are 'real' toilets; they flush, they are usually made from white ceramic, and all the other things one expects from a modern toilet.
You can go to this site for an animated example of how one works. It is interesting... I guess. It does not mention that wiping yourself can be awkward until you get used to the new positioning, but it does make a point of mentioning that keeping your balance can be hard. Westerners do not usually exercise the muscles one uses for squatting, and the first time you use one of these toilets, you should be prepared for cramps and/or stiffness in your legs. Be careful.
Japanese toilets are said to be more ergonomic and cleaner than western toilets. More ergonomic because humans evolved to poop squatting, not sitting, and cleaner because your butt does not touch the toilet seat, which is especially nice in public toilets. They are also slowly becoming extinct, as south-east Asia, and the rest of the world, Westernizes. They are still found in many countries in Asia, Africa, and the Middle East, and may occasionally be found in some European countries, including Spain and Greece.