Look here to find vegan food in convenience stores, as well as the more vegan-friendly convenience store Natural Lawson, vegan fast food, festival, cafe, and airport food options and vegan-friendly hotels and lodgings.
Is it Vegan? (Japan)
For your vegan life in Japan
Is it Vegan? (Japan) 
Please, update this section! hahahaha
I just found out chuukaryouri is good in these cases =)
Onigiris… i think they have something they take from milk =S At least the ones I saw
Fruit is always a good option, and salads… lol
Anything else? =P Just arrived a few days ago
Thank you for using our website! A section on convenience store food is coming soon!! As you say, fruit and salads are good options. There are also things like nuts, chestnuts and plain potato chips. Some onigiri also seem to be vegan – perhaps the ‘milk’ kanji you saw was emulsifier: 乳化剤 (although I believe this can be from either plants or animals). Places like Kappa Sushi have cucumber rolls, pickle rolls, eggplant sushi and inari zushi. There is also potentially vegan soup in some vending machines (see our section on soup). Please let us know if you make any good discoveries 🙂