So serious has the problem become that the National Police Agency (NPA) has made its concerns that hundreds of firms have mob connections public in a policy document, the Times reports.
Otherwise known as the "Japanese mafia", the Yakuza is understood to have launched a pre-meditated assault across the entire corporate sector.
Many of the criminals are using the financial system for their own ends - creating front companies and buying up stock in order to illegally manipulate share prices for profit.
This is a marked change in direction from the mafiosi's previous activities, which centred on drug dealing and prostitution.
The move has led to a "disease" which will "shake the foundations of the economy", the NPA warned in its white paper.
Speaking to the newspaper, Yakuza expert Joshua Adelstein commented: "The police are worried, but they are understating the problem. Organised crime has made tremendous inroads into the Japanese financial sector.
"The bad guys now have everything in place to manipulate the stock market."