Owned by Japanese people or serving Japanese food?
There are loads serving Japanese food, with my favorite being Ramen 38 Sanpachi. They use pork and do have much more than ramen on the menu!
Perhaps the second (a diatant second) would be Sushi Tei. Their food is pretty good, but I don't think it is good enough to justify the prices.
There was a Japanese owned restaurant I used to go to on Setiabudi, but they closed years ago. There was another Japanese owned place too, but I'm really drawing a blank on it.
Of course there are a few chain restaurants serving Japanese food with reasonable prices and quality, but those would be the same as they have many major cities: Zenbu, Sushi Groove, etc. Sushi Tei is actually a chain as well, they just have slightly better food and higher prices.