Many foreigners traveling to Japan for the first time should try to be very careful, because Japanese are very polite. In truth, they are very forgiving of foreigners but there are things that offend them so make sure to avoid the following things:
Not taking off your shoes
The Japanese are easily annoyed by loud and boisterous behavior, but this is especially true for public places. You are not forgiven for being loud and boisterous when drinking in an izakaya or karaoke bar, but on trains, buses, and on the street, try to keep the level quiet! (Especially if you are traveling in large groups).
To be late
They take the appointment schedule literally. If they say, "Let's meet at 4:45," you are literally expected to be there on the spot. Being late can be annoying and even disrespectful.
Not giving your seat to an elderly person in public transport
If you see a pregnant, elderly and disabled woman on your train or bus, that means you are in front of the reserved seats. For obvious reasons, anyone in their 60s should be given their seat, especially if they look like they are struggling to stand up.
Sit when offered to do so
Visiting a person in their home, office, or even a restaurant is usually a good way to sit down only after a seat is offered. Keep in mind that the Japanese are well aware of the "politics" of who sits where, so it is a good idea to wait until you are told where to sit.
Do not litter
The Japanese are the masters of cleanliness. If garbage is thrown in the street, then you will be very offended. Also, when eating a meal you have to make sure not to leave little pieces of rice or other foods.
Not pointing people
Although this is generally rude wherever you go, it is good to note that hand gestures are very different in Japan. For example, when pointing to a person, you don't have to point your finger at him or point to some. If you want to indicate to someone who is next to you, you have to put your palm up, keeping your fingers closed.