Things may be different in Japan, but you do not understand how this works in the US. Investment in research doesn't mean you own the work.
Having a solid IP assignment agreement with a scientist and a strong cultural and political expectation of ownership is what determines who owns IP. Without a legal IP assignment contract (wording which has survived a court challenge, and an agreement in which both parties benefit - this is where investment comes in), the work IS owned by the inventor.
In terms of investment, you have a physicist who has invested $500k in specialized training (the current estimated personal cost of scientific training over 10+ years). In the US, the government funds the majority of training and early research (~$2-4M) through universities (who on average come out ahead financially in this arrangement). In the last stage, a company funds the final research leading to development (~$500k-$1M).
Who owns the patents to the work? In the US, the fundamental patents are owned by the university that trained the scientist. Universities generally don't invest in research, they get someone else to pay for it. Big universities generally don't count lab scientists as employees anymore (they're all contractors and 'visiting scholars' now). But, they do secure solid IP contracts from every contractor, student worker and professor who works on campus.
There's a very good argument that all of these government funded university patents should be owned by the government. Government grants generally include clauses claiming some ownership of IP generated. It's too bad that politically, that's not something that can be enforced.