The difference is that rather than being explicitly "we don't want immigrants," Japanese society is a fairly closed one that relies on a niche language. No language, no acceptance.
Beyond that, for educated people to immigrate to another country, you need to have a job market that accommodates those people; Japan doesn't really have that. The wages and benefits aren't competitive and the pension system is unfriendly to immigrants. Additionally, you really need a good grasp of the language.
You can also see another recent post of mine about the difficulty of making friends in Japan, which is another thing that makes it difficult for people to come here. It doesn't help that people who come here often have a mediocre grasp of the language, which makes things more difficult and encourages them to live in a "foreign bubble," which will often lead to depression when it pops.
On the up side, the Japanese immigration process is INCREDIBLY simple, especially compared to the US one (which I've heard about second-hand from Japanese people). In order to work here, you basically need a university degree and a job that pays more than around $25k/yr -- with those, you're a shoo-in within a month or so.
Getting PR in Japan is pretty much just a matter of having lived there for 5 years and not have broken any laws.
Compare that to when my wife immigrated to Canada. Despite her speaking English, coming from an economically developed country, having a University degree and years of professional work experience we still needed to wait for over a year and it cost $2000 for everything involved.
If you want to work and live in Japan, legally speaking, it's incredibly easy. The difficulty of integrating into society is the tough part. Even with a fluent grasp of the language, you'll always be an outsider.
To say "Japan doesn't really want immigrants" is kind of accurate though. Japan relies on its closer culture to keep immigration low even though it may be more subconsciously and not a formal government policy.
Yeah, this is the part I always think of when I hear people here grousing about standing in line to submit visa paperwork or whatever. It's annoying to waste a day at immigration, but I know people in America where one partner is an American citizen and the other is an immigrant, but they've been watched and scrutinized and interviewed for years and years before the immigrant partner could get a green card. It's pretty ridiculous.