I am not too familiar with independent Japanese watch makers. There are lots of smaller brands making timepieces in Japan aside from the big three (Seiko, Casio, and Citizen), but most of those are less expensive or novelty pieces. Here is a high-end independent Japanese watch maker you should be familiar with named Hajime Asaoka - with a brand of the same name.
His watch is the simply named Hajime Asaoka Tourbillon and it is a very attractive timepiece. The design is actually more architectural and art deco than it is traditionally Japanese. Not that there is anything wrong with that, but aside from the name and "Tokyo Japan" label on the dial, there isn't much to let you know this is a fine Japanese instrument.
For me the design quickly becomes appealing as you begin to identify its values. This is about an expression of technique and industrial design. A good start is to look at the tourbillon bridge. It is formed out of a single piece of steel that has a bar through the middle and angular segments on the side. Simple? Sure, but to achieve that each needs to be delicately hand polished as this is a technique I don't think that most machines can accomplish.
The tourbillon itself runs at 18,000, making it slow enough to gracefully view. The design of it is clearly something that isn't European. It feel like it is more a celebration of small steel parts and machinery, and it is about just making a tourbillon. Hajime's website is skeletal with almost no information about him or of the watch itself. He e-mailed me with just a few information tidbits, but through his humility is the watch that clearly illustrates his talents.
I love the dial of the watch. It is three-dimensional with a lovely vertical texturing and simple yet satisfying design that is both legible and artistic. Most elements on the dial remind me of buildings. The watch case itself is in steel and 42mm wide. It is rather thick at 14.80mm, but you won't hear me complain about that. The case appears basic at first, but is actually really well done with its rounded sides and masculine crown. The movement itself is basic, but an expression of conceptional execution. You rarely see those with the talent of the Japanese create versions of what the Swiss are best known for. Assuming Hajime had a large team and lots of budget, I would be interested to see what he could come up with.
As far as I know the Tourbillon is Hajime Asaoka's only wrist watch at this time. The hand-crafted mechanical watch isn't cheap either. In steel it retails for 6,825,000 Yen, which is about $87,500.