OK, here's how it works.
When you see a Japanese player at the PT practice hall, he/she got there by one of these way:
1) National team/Junior national team
Funded by JTTA. Need to be in the squad to be eligible.
Eg. Mizutani, Niwa, Ito.
2) Elite Academy
This is the big one. Funded by JOC. It was formed with the new National Training Center which takes juniors from TT as well as other sports (Fencing, Wrestling etc) and train them with state of art facilities and coaches until 18. It's been hit & miss for TT and it's only recently that they started to develop top players.
Eg. Harimoto, Hirano, Hamamoto.
3) Schools/Corporates
They have been the biggest development force in Japan for a long time. Only a few years ago, majority of mens NT are from same high school(Mizutani, Niwa, Matsudaira, Yoshida). They too have a set budget so that the students can gain international experience as well as earn ranking points. Corporate teams usualy sign a contract with players which allow them to participate in several tournaments par year.
Eg.Ueda, Morizono.
4)Individual sponsorships
Technicaly there are 2 subtypes that fall under this category. One is a professional player who earns a living by playing abroad and hires his own crew but only Mizutani does that. The other one was started by none other than Ai Fukuhara. She was attracting nation's attention since she was 4 as a TT prodigy and turned pro by the age of 10. Since then, she formed Team Fukuhara and was copied by other top women (Ishikawa, Ito, Hirano).
Of course some of them overlaps(Ishikawa was under 1/3/4 until 18) and that's why you see huge number of junior players as some are funded by JNT and some by Elite Academy. JTTA has stated that the selection criteria for WC and olympic is world rankings so that's why they tried to particpate in as many PTs as possible.