This rule of toilet use varies in each country of Asia.
There are some countries where you are not allowed to flush used toilet paper and other disposals. You should be aware of it and check beforehand if you tour around Asian countries.
So, what you should know about toilet use in Japan is,
You are allowed to flush only used toilet paper down the toilet. Other non-water-soluble disposals, such as sanitary napkins and tissue paper, are to put in a small rubbish bin placed in each toilet room.
The bin is called Sanitarii (sanitary) Box or Echiketto (etiquette) Box in Japanese
Related article (digi-joho TOKYO TRAVEL) : Japanese Style Toilet