You can throw toilet paper in the toilet in Japan.
Toilet paper is designed to be flushed down the toilet after use as toilet paper is made to dissolve rapidly in water.
Japan's sewer systems are capable of handling toilet paper, although some other countries have poor sewer systems and so they advise against throwing toilet paper down the toilet in some other countries.
But in Japan it's acceptable to throw toilet paper in the toilet and flush it down and it's also encouraged too.
I was at a restaurant in Japan once and there was a sign in the restroom that wanted you to throw the toilet paper in the toilet and not into the trash bin.
Throwing the toilet paper in the toilet and flushing it down is much more sanitary than throwing it in the garbage bin.
Just avoid flushing other things down the toilet like baby wipes, napkins, paper towels, paper diapers or pads down the toilet in Japan or anywhere else as these can clog the toilet.
Even flushable wipes should not be flushed down the toilet as they really are not flushable and can clog up a sewer system.