Wearing flip flops in public places such as on the street or in a restaurant is less common in Japan than in some other countries, as it is considered more casual and less appropriate for formal occasions.
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A common rule of thumb is if the place is culturally traditional, has tatami mats, or is someone's personal space like a residence, then you should take off your shoes. Otherwise, it is likely okay to leave them on.
In summer, many people choose to wear longer skirts or slacks instead of shorts, and few wear tank tops. Pack clothes that aren't too flashy and make sure they're appropriate for the activities and the season you have planned. Bring a dressier outfit if you plan on eating somewhere nice.
All footwear is fine. Heels , flats, boots, sneakers, sandals. The only thing I don't see a lot of is older sneakers -but that doesn't mean don't do it. You just don't really see “well-worn” dirty sneakers outside of the running track or gym but .. it's not the end of the world if that's what you like.
In conclusion, leggings can be worn in Japan, but it is important to keep in mind the cultural norms and etiquettes. When wearing leggings in Japan, it is recommended to pair them with a long top or tunic and avoid wearing them to formal events or religious sites.