Japanese students take their shoes off to keep the school clean. The reasons and significance for this have to do with teaching students responsibility and respect. To this end, Japanese state schools do not employ janitors or custodians. Keeping the school clean is the students' responsibility.
It's common knowledge that Japanese people remove their shoes before entering a home in order to protect the bamboo floor mats (or "tatami") from soil and wear. What is less commonly known is that they follow the same custom when entering certain public buildings, even though such buildings may have no tatami flooring.
When entering a state school, everyone (students, teachers, employees and visitors) take off their shoes just inside the entrance and put on slippers or special indoor shoes--regardless of status or authority. In this way, taking off shoes acts as an "equalizer."
Japanese state schools do not employ janitors. The Japanese education system (and Japanese citizens in general) believe that requiring students to clean the school themselves teaches respect and responsibility.
One of the more intriguing results of making students responsible for maintaining a clean school is that with no janitors to clean up after them, students in Japan do not learn any of the condescension for janitors, custodians or cleaning staff that is so common in other countries. By having students clean schools themselves (and taking off shoes is one way of keeping the school clean), students do not see themselves as "above" such work.
Students remove their shoes at the entrance of the school. They place their outdoor shoes in a small, square shelf called a "geta bako" and put on "uwagutsu" or indoor slippers. The "geta bako," or shoebox, is used primarily for storing shoes, but it doubles as a kind of informal letter box in which notes for the student can be left. Students in Japan do not have lockers of their own. These shoe boxes are the closest students come to having a private place to keep their personal effects. Many people, however, consider the "geta bako" dirty (from the shoes) and avoid leaving notes or other effects there.
The "uwagutsu," or indoor slippers, tend to be soft canvas tops with rubber soles. These indoor slippers protect the students' socks from unnecessary wear and tear, provide extra traction on the linoleum floors, and provide a little extra warmth in winter in the unheated classrooms. Even grade school classrooms are unheated in winter, as this "toughens up" the children and teaches them not to expect too much in the way of creature comforts.
Every public (and almost all private schools) in Japan requires students to wear uniforms. In Japan, the requirement that all students wear a school uniform is meant to enforce a sense of equality and teamwork among students, to ban the public exhibition of status symbols such as fashionable clothing, and limit in-school distractions to education. The use of indoor shoes ("uwagutsu") and slippers is simply another means of enforcing a uniform dress code. It should be noted, however, that students do not view this as a requirement: taking off one's shoes before entering school is simply what people do.
Wear and Tear
Another reason for students to take off their shoes is to prolong the life of their outdoor shoes. The indoor slippers and shoes are usually much cheaper to replace than the outdoor shoes.