Yes, you can wear leggings in Japan. Leggings are a common fashion item in Japan, especially during the colder months. They are comfortable to wear and can be paired with various outfits.
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Avoid things like tank tops, shorts, and mini-skirts. Opting for more conservative clothing is always a safe bet even if you don't plan to visit temples or shrines. It's also generally frowned upon for women to show cleavage. Clothing with offensive messages or designs.
In general, you will rarely see Japanese women with spaghetti strapped tops or even shoulders out. That doesn't mean its a no-no in Summer though – if that is what makes you most comfortable. As for showing cleavage? It rarely happens (even in fancy situations like weddings etc.)
Try to be mindful of the type of shoes you're wearing, as certain shoes, such as sandals, might not be allowed in some indoor spaces. If you're given slippers at the entrance to a building remember to wear them inside only! We know they're comfy but these aren't meant for sightseeing or as a souvenir!