Bread in Japan is almost always prepared using milk or dairy products, and often even includes egg. It is very difficult to find dairy-free bread for purchase in Nagasaki, and it gets more impractical for people in the countryside. Even many breads in the grocery store advertised as soy milk bread still contain whey powder. The bread that can be most often found vegan is baguettes, but even those usually have dairy in them.
Quite a few pre-made pizza crusts and tortillas are safely vegan.
Vegans and people with dairy allergies who want to eat bread should seriously consider buying a bread machine. Bread machines can be as cheap as ¥2000-¥5000 at second-hand shops, and if you use a scale (any cheap scale will do) it takes 4 minutes to get all the ingredients together; then the bread machine does all the work. The ingredients are cheaper than buying bread which in the long run makes up for the cost of the bread machine. Homemade bread can be stored on the counter or in the freezer. (Homemade bread is also an excellent gift, for anyone struggling to think of gift ideas).
Ordering Food Online
Amazon Japan, Rakuten and iherb.com are great places to order vegetarian/vegan staples such as nutritional yeast, flax seed meal and chia seeds. There are also some vegan treats (often meant for people with allergies) available on Rakuten (they can get a bit pricey though).
What to do about Kyushoku (school lunch)
For Pescatarians and Flexitarians
Pescatarians and flexitarians might be able to get away with eating most of the kyushoku. Kyushoku has quite a bit of fish in it and sometimes has red meat. In Nagasaki prefecture, kyushoku occasionally has whale meat (鯨、くじら, kujira).
Most schools are very understanding if you tell them you don’t feel comfortable with eating meat. So long as you clearly explain that you might not eat all of the kyushoku and are nice to the people dishing out the food, you should be alright.
For Vegetarians and Vegans
Kyushoku really isn’t vegetarian or vegan friendly. Unless you want to eat kyushoku and maintain your vegetarianism/veganism outside of school (which is totally fine!), you will probably have to bring your own lunch. If you want to make it easier on yourself, most schools have no problem with giving you only rice, and then you can bring your own veggies/tofu to put on top (pro-tip: if you pack frozen veggies with a sauce in the morning, it thaws by lunch). Sometimes kyushoku has bread (which very likely has milk in it) instead of rice, and for those days it’s a good idea to bring rice packets (available at most convenience stores) that you can heat up in the microwave.
Eating out at Non-Veggie Places (Work Parties- Enkais and Nomikais)
Even if you didn’t call ahead, if you speak enough Japanese to convey what you can and can not eat, it is worth asking if you can eat anything, or if some option on the menu can be modified slightly to be made vegetarian/vegan/etc. Many places are surprisingly accommodating, but be aware that it isn’t always possible and you may just have to munch on some edamame.
Mosburger, Coco Ichibanya, and Mister Donut all have vegan options as part of their regular menu.
Soba and Udon
Soba and udon places often have zaru soba or zaru udon available, which is just noodles with a separate cup for katsuodashi. Since the cup is separate, you can often ask soba and udon places to omit it so you can use soy sauce instead. Some chain udon restaurants have hot water servers so you can bring your own hondashi (dashi pellets that can be mixed with hot water), ask servers to omit the dashi, and mix your own dashi at your table.
Sushi
Most sushi places have vegan sushi, such as kappamaki (cucumber rolls), natto rolls, and various pickled vegetable rolls. Many sushi places also serve eggplant, and sometimes if you don’t see it on the menu you can ask about it.
Pasta
Some pasta places use cheese and meat in their tomato sauce, but it is well worth asking as many do not.
Calling Ahead
Many restaurants are accommodating and willing to make a special meal if you call ahead a few days before. This often works well for enkais and nomikais (work parties) so long as you are communicative with the person planning the party.
Veggie-Specific Places
Rota Café （ロタカフェ）(currently closed)
Nono Hana （野の花）(small grocery shop with vegan bread and other organic fare)
Café Tida （カフェティーダ ） (reservation only and far from Nagasaki city center)
Unzen Jigoku Café （雲仙地獄カフェ）(possibly closed or on hiatus due to a mud slide)