Because in Japan Islam is not the majority religion, halal-certified food is still limited. But Muslim tourists need not worry, because there are simple tips for choosing food, so travel to Japan is still exciting.
Some Japanese specialties that are relatively safe for consumption include Sushi (except Unagi and Anago which in sauces usually use Mirin and sake), Sashimi, Soba, Udon, Tempura (avoid using the sauce because it generally contains sake and mirin), Yaki Sakana, etc.
Another alternative is to go to Muslim restaurants such as Arabic, Pakistani, Turkish or Malaysian cuisine. There are quite a number of restaurants that provide Islamic dishes in major cities in Japan. Information on these restaurants can be found on the following site: Japan Halal Association http://www.jhalal.com/restaurant-list
Although there are many traditional Japanese foods made from fish, there are some Japanese dishes that generally use pork or pork broth. For example, ramen, tonkatsu, gyoza, okonomiyaki, some types of curry etc. Foods from the Okinawa region use a lot of pork and processed foods, such as Goya and Okinawa Soba.
In addition to pork, other meat-based foods (beef, chicken, goat, etc.) also need to be considered, because the possibility of meat being served is not slaughtered with Islamic procedures.
Tourists are also advised to be careful of foods that might use sake (Japanese wine) or mirin (sweet cooking sake) as a cooking spice. For example in teriyaki, yakitori, etc.