As someone who waged an epic battle against mites a few years ago, I genuinely feel your pain because you are in for a long, awful ordeal. But let me share a few things I learned first before going into the eradication methods.
One, confirm they are mites and what type. In my case, mine were red mites. Long story short, I was babysitting a parrot in my penthouse condo, where I kept the windows and balcony doors open all day, and the little shit would happily call out to all of the stray birds and invite them into the apartment while I was gone, even intentionally throwing birdseed toward the balcony to entice them in. That ended up with feral birds coming into my condo and bringing their mites with them. Little fucker ended up with mites all over his wings but it didn't seem like he gave a shit...but he didn't seem too pleased getting doused with mite poison every day as a consequence and was very vocal about how unhappy he was with the treatment. Mite bites are usually on your lower extremities, often on thighs and in the groin area, and can usually be identified by being two or three small itchy bumps very close together. I guess mites will bite you, not like the taste, but bite you again a couple of times just to make sure. But that also means that mites won't infest your unit just for the sake of biting YOU, because they don't like humans. They'll stay near a host, which is usually feral birds.
Two, that means you need to check the exterior of your house/apartment. Most commonly, mite infestations will be due to a birds making a nest somewhere that mites spread out in search of food while the nesting bird is gone. A/C ducts, under the eaves of your roof near windows, etc., are places to check for feral birds/animals nesting or making homes. Those need to be wiped out or the problem will never go away. Again, mites are there for a source animal, not you. Remove the source, and they'll eventually leave.
Three, once you've identified the source, you basically need to destroy every area mites can hide...and with tatami, that is the PERFECT hiding place and I'm thinking you may have to just dump all of your flooring. In my case, they were hiding in the hollow structure of the parrot cage and also in my carpets and rugs. All were tossed. Not wanting to poison myself or my apartment, I tried an experimental cedar oil treatment, which was basically a $500 "fogger" and a $150 gallon of cedar oil, which I then used to fog up my entire apartment three times. If you've ever seen videos of guys using foggers to destroy wasp nests, that's what it looked like...and then my unit reeked of fresh cedar for weeks. I've read stories saying that the cedar oil treatment is a hoax, but the mites were gone after that.
It goes without saying, I also removed the host (parrot). Fucker went home in a new cage, covered in unpleasant mite dust and bitching up a storm, and I never volunteered to watch him again.
YMMV, but I think at the very least you'll have to fog/bomb your apartment and I have no idea what those options are in Japan. Shit, I might consider just moving apartments. Another pointer, mites are nocturnal animals and generally come out at night to bite you. They crawl up the legs of chairs or your bed and up your legs and like to bite in warm, dark, moist, covered areas (hence the bites around your groin). What mites don't like, however, is Vick's Vapor Rub. I'm assuming you can get it in Japan. I used to rub it around my ankles, knees and wrists and that would generally lower the number of times I got bit each night. Not sure what you can do if you're sleeping on the floor, but what I started doing was sleeping on my sofa and also rubbing Vick's on the legs of the sofa to keep them from crawling up.
If/when you do fog/bomb your apartment, remember that mites like to sleep as close to their prey as possible. That's why they were generally nesting in the crevices of my parrot's cage (inside the frame, under the newspaper, under the slide-out tray, etc.) and will also hide near you, so in your bedframe, crevices of your mattress, headboard, etc. When I fogged my apartment, I dumped my mattress and then repeatedly cedar fogged the bed frame and headboard, along with everything else in my apartment. I dumped my comforter, sheets, and any linens you are inclined to keep I would first put in an airtight garbage bag for a month and then wash in hot water and bleach.
Again, remove the source and the mites will leave. That means if you can figure out where they came from (bird nest outside your window) and then you leave your apartment for a few weeks, they'll most likely leave as well. Short of doing that, you just have to kill them all.
Good luck with that. Mites are a fucking curse, for sure.
