"The company is charged with illegal discharge of a harmful substance -- oil -- from the vessel, failing to notify MNZ [Maritime New Zealand] of the discharge, and failure to notify a pollution incident," the regulator said Tuesday.
Combined, the maximum penalties for the charges are a fine of $300,000, two years in prison and an additional fine of no more than $20,000 per day the offense was committed.
"As the matter is before the courts, MNZ is unable to comment further on the detail of the case," the authority said.
Sanford said it was conducting its own investigation into the claims made by a former Indonesian crew member of improper use of machinery on board the South Korean-flagged fishing vessel Pacinui.
The case is due in court Monday.
The cargo vessel MV Rena struck a reef off New Zealand in October 2011, spilling about 2,000 barrels of oil into the Bay of Plenty.
Daina Shipping Co., the ship's owner, entered a guilty plea to charges related to the discharge of harmful substances and was fined $300,000.