Chopsticks
In Japan, most food (except soup) is eaten using chopsticks only (although some restaurants may have spoons and forks available).
Table etiquette
It is customary to lift your bowl with one hand while eating when at a Japanese restaurant.
It is considered bad manners not to lift your bowl while eating or drinking soup, or to incline forward to a plate, then eating from the plate afterward.
Hold your bowl by lifting it with your left hand. Keep your fingers flat and stretched, use your thumb to grip the bowl at from the edge, and keep your remaining four fingers underneath the bowl to provide support.
Holding it this way will keep your hands from getting burnt no matter how hot the contents of your bowl are.
It is generally considered good etiquette to refrain from making noise when eating, but sometimes it may be considered tasteful to make a slurping noise when eating noodles such as soba or udon.
Leftovers
In Japan, it is considered good manners to eat everything you are served and to leave behind an empty plate.
If you are invited for a meal but leave some food untouched on your plate, you may need to let your host know the reason, whether you do not like certain types of food, are full, have certain allergies, or have religious dietary restrictions.
Mealtime conversations
Avoid talking with your mouth full. Swallow your food first before speaking.
Depending on the ambiance of the restaurant, you may also want to avoid talking in a loud voice.
Always take note of your surroundings and act in a manner appropriate to the context and situation.
Mealtime traditions
In Japan, it is customary to say "Itadakimasu" before a meal and "Gochiso-sama" after the meal to show appreciation for the food.
After the meal, say "Gochisou-sama" as a token of appreciation.
