The skirts themselves aren't that short (only in anime, really).
What happens is that Japanese girls find their skirts too long. So they either fold them up or raise them a little higher.
Most Japanese schools have their own "seifuku" (school uniforms), and especially the girls' uniforms have evolved into a variety of unique styles.
One of the striking characteristics of some school uniforms is the short length of the skirts.
The culture of wearing short skirts began when Gyaru culture was at its peak in the 90s, influenced by the legendary Japanese pop star with her super short skirt, thin eyebrows, and bleached hair.
The girls at the school adopted it for their school uniforms and began to shorten their skirts.
How do I do that?
It's easy.
Basically, there are three ways.
1. Cutting.
2. Folding the skirt at the waist
3. Using a "skirt-belt", as in the figure below.
However, cutting the hem of a skirt is risky, as there are weeks of "skirt length checks" or events held randomly at school.
If you are caught wearing a skirt that is shorter than permitted, you will be punished.
Therefore, it is more common to fold the skirt over the waist or to wear a "skirt-belt".
Here's a video showing how to wear a belt skirt.
It's super easy!
Fold the waistband inwards to keep the pleats nice and pull the belt up with the skirt until it's short enough for you.