(1) Japanese bigcorps have extensive on the job training programs which bring relatively specialized new grads up to speed. In fact I think it does a great job at getting nearly all new hires up to median performance within the company. Think of it as relying on mass producing "good employees", rather than focusing on finding "great employees".
(2) Japanese bigcorps are organized such that promotions and pay increases happen based on seniority. This is especially the case at the lower ranks, where everything is very methodical and planned out. Promotion cycles tend to happen every 3 years, with boolean results. Raises happen methodically every year according to HR's tables (though these get phased out when you get more senior -- part of the cost cutting efforts in the last 20 years).
Combine these two factors and companies want young, cheap "good enough" talent to join their company, after which they will train them according to their corporate flavor. Hiring a PhD means that you have to pay them higher than the undergrad, even though you're going to put them both through the same training cycles. Unless there's a really good fit between the doctorate candidate's research and what a team wants (or lab-corporate connections), companies will shy away from hiring PhDs.