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.
There is Qoo Qoo sushi buffet (started in Korea), that has tons of sushi that opened in October. It was actually pretty good when we tried it October. One of the better sushi buffets I’ve ever had.
Of course a Japanese guest would probably think most of it was unworthy.
I’ve had high end sushi at the Japanese restaurant at the JW Marriott in Jakarta. It was good, but the price was pretty high, 400k for a basic bento box. Way more if you wanted something more elaborate.