3 providers bill in JPY, listed alphabetically. Split across shared hosting and vanity hosting, across 1 country. 51 records do not record this field, and cannot appear here either way.
L
- Lolipop!
Japanese rental server from GMO Pepabo, selling shared hosting for personal and small-business sites through its own control panel.
O
- omg.lol
A personal internet address bundling a profile page, email forwarding and a handful of small web tools for one flat yearly price.
X
- Xserver
Japanese rental server company selling managed shared hosting, with WordPress tooling, automatic backups and free SSL included across the range.
Who is the best host that bills in JPY?
Hard to say without knowing the project. A free tier matters for a side project and barely at all for a shop that loses money every minute it is down. Read a few records side by side; the guide says where to start.