Comment by maxgashkov

I know a few folks personally who got rejected for PR but got approved for citizenship. First, both of these get handled by different branches of government with the different screening guidelines (often not published). Second, perception differs: for a long time PR was viewed as something like 'all the benefits of living in Japan without any consequences', so the income requirements were stricter etc. (albeit all of this is changing now and it's difficult to say what will be the final state).