It looks like JTB has started a service to allow people to apply for races from overseas. I did a search on their site and only found the Abashiri marathon for races in Hokkaido. Hopefully more races will hook up with this service in the near future.
You can find the page for the Abashiri - Ohotsuku marathon (Sept 25) here:
https://jtbsports.jp/en/events/events-detail.php?id=4810
2016-09-26 Update: Please check the comments on this post for more information about the event.
Supernova has provided us with a link to the English guide for the race.
https://jtbsports.files.wordpress.com/2016/09/e88bb1e8aa9e1.pdf
If for some reason that file gets taken down, here is a backup:
https://app.box.com/s/1fkpyq6mhtf7x7btw2d7s0ye8ahk1h59
