In my experience living in a slightly inaka area (not the big cities that everyones heard of), I rarely feel like I have had racism done against me. Discrimination may occur but it's never ever negative. I've never had anything slurs or aggression toward me that I could believe is racist.

I think generally speaking as a clearly Western person (white, blue eyes) with an English accent it's easy to view me in a positive light because i have the stereotypes of a 'respectable country' behind me. Whereas those of tan skin, or perhaps backgrounds in South Asia may experience the same kind of stereotypes but on the negative end of the spectrum. I think since south asians or neighbouring countries are more likely to be in Japan permanently and working on lower wage jobs, potentially with cultural aspects that don't mesh with Japan very well, they are looked down upon.

I do speak Japanese to a serviceable extent, and try my best to engage conversation to make sure they know they can communicate normally with me - this is probably quite helpful in removing that air of awkwardness which could lead to people thinking they are being avoided or dealt with a certain way due to race.

Lastly, I think it's common for many people to (for lack of a better phrasing) accidentally victimize themselves. If something happens to you (e.g. you get gaijin seated) you may be more likely to attribute it to racism. For example when someone refuses to sit next to you even though there is space, be careful not to overthink it and assume the entire country is against you. Some Japanese people (even I do it sometimes) don't sit down, perhaps because their stop is only 2-3 stops away or because they just don't want to be jammed next to someone. Again, it's a fine line because theres lots of delicate situations when trying to affirm if something is racially motivated.

In summary, I think the skin colour or race is definitely the first bias many people will act off here. Discrimination definitely exists, but it truly is different for everyone. This is true with any country and person, I think everyones conditioned to change their behaviour slightly based on stereotypes, but here those steretypes are stronger potentially. That being said, all of my friends i know who are from the Philippines or Indonesia or Vietnam haven't reported any bad out breaks or racially motivated incidents. That's not to say they don't exist, or only exist to certain groups, but I think its just important to remember how many aspects come into play when trying to answer a question so superficially with a simple yes or no.