Using  Chopsticks
You don’t have to eat with chopsticks but everyone does, so why don’t you? Chopsticks are by far the best implement for getting around the bones when eating fish. There are a couple of things you should know when using chopsticks.

Generally you shouldn’t rub them together to smooth them off, it’s considered rude. Never leave your chopsticks in a bowl or stab your chopsticks in rice and leave them standing up. This has some similarities to proceedings in a Japanese funeral and is considered highly disrespectful (they pick up the bones with chopsticks).  The best place to leave them is on the chopsticks holder, or lay them on the chopsticks paper cover on the table, or on a plate or bowl (if that is all there is).

Japanese Eating Habits
Slurping is not generally considered rude. The fact is that there are a lot of noodles and soup served piping hot in Japan. Slurping helps to draw air over the food as it goes into your mouth and helps to cool it down. Japanese will even make slurping noises with hot rice if they are in a hurry to get it down. If you happen to dine with the emperor then maybe refrain. Use your discretion here.

When Japanese dine out (which they do a lot) they always wait to take a drink. Generally the whole tables glasses are filled and then someone makes a brief toast or says kanpai. Always wait until everyone else drinks to drink. It is also polite to fill other people’s drinks. These days it is a good idea to meet their eye and confirm if they want any more when you refill as some people don’t like feeling pressured to drink.

Food also is mostly placed in the middle of the table and you take small portions onto a small plate called a torizara for yourself. If you are at a big table and it would be difficult for some people to take from the dish near you then you can ask if anyone wants some, or just dish up a couple and pass them around.