The EU Commission said Canon breached rules by using a so-called "warehousing" two-step transaction structure involving an interim buyer to buy the company prior to obtaining relevant approvals.
Ten percent of Canon's annual revenue would be roughly equivalent to $2.9 billion.
The $6 billion deal, completed late last year, raised eyebrows at the time due to the unorthodox method which allowed Toshiba, which was struggling for cash after an accounting scandal, to book proceeds in time for the financial year-end in March.
Rival bidder Fujifilm slammed the deal as a "mockery of the law".
Canon said in a statement that it would respond appropriately, but declined further comment before regulators make their final decision.
Last month, EU antitrust regulators hit Google with a record 2.4 billion euro fine for favouring its own shopping service, so it is proving a lucrative month.