My mother kissed me on the lips when I was a kid. I didn't kiss my kid at that age, but that's because I'm a bit of a germophobe, not because it would have been weird or something. His mother did kiss him, though. I've seen friends do the same with their kids. It generally tapers off as the kid approaches teenage years. There is absolutely nothing sexual about any of this - it's just parent/child affection.
That's in rural Oklahoma, though. Japan? Seems a bit odd.