I'm not Indian but brown. In five years of living in Tokyo, the worst I've experienced is:

Twice being stopped by cops near Shibuya Station and asked to show ID. Once I was coming back from a run and had a hoodie on. The other time it was really late at night, I may have been walking home a little tipsy lol.

On a couple of occasions people randomly assuming I work for an IT company. Though in both instances it was a non-Japanese person. And well, it has to do with the fact that there *are* a ton of Indian IT professionals in the Tokyo area.

In the grand scheme of things these are quite mild. And some of the stories I hear from guys who've been living here 25-30 years from when they first got here, things are a whole lot better. For example, I've never been turned away from a restaurant. Never entered a real estate office and been immediately asked to leave. Though landlord discrimination against non-Japanese is still pretty common. But that's for any foreigner period, not specifically brown people.

In the hospitality/tourism area, people have always without exception been extremely polite, helpful, and cordial.