Isn't "5M JPY investment" (45k USD) the requirement for the visa, not the cost?
The money is still held by your company and you can own the stock, so it's not like you are "spending" it.
edit: After checking a relevant Japan ministry of justice webpage [1], 5m yen is given as an indicator, which is why I suppose it is the value given by most lawyers.
[1]: http://www.moj.go.jp/nyuukokukanri/kouhou/nyukan_nyukan20.ht...