Most Japanese women wear heels even with casual clothes. I wore Birkenstock sandals and was very comfortable everywhere I went. Take a pair of nice socks with you in case you are required to remove shoes.
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If you are not wearing socks, it is polite to bring a fresh pair of socks to wear after removing your outdoor shoes because entering someone's house barefoot is not considered well mannered, although acceptable in informal situations. Slippers can generally be worn anywhere except when entering rooms with tatami floor.
Instead wear: Slip-on shoesEven though they're perfect shoes to wear on vacation, trainers, boots, and Birkenstocks will only slow you down at the airport when you are inevitably asked to remove them to go through security.
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.
Generally, it's a good idea to wear easy-to-take-off, comfy shoes to the airport, especially if you pass security checks. Slides are a fantastic option for this because they are often comfortable to wear and are simple to put on and take off. Imagine trying to exit a burning aircraft in flip flops.