The November storm in the Kerch Strait, which lies between Russia and Ukraine and connects the Black Sea and Sea of Azov, sank four ships with a total of about 7,000 metric tons of sulphur on board and damaged two oil tankers. At least six sailors died and around 2,000 metric tons of fuel oil spilled into the sea.
"Oil products spilled into the sea during efforts to bring the Kapitan Izmail afloat. Those guilty will face charges," the ministry's press service said, citing Oleg Mitvol, deputy chief of the state environmental watchdog.
The transport prosecutor's office in Russia's Black Sea port of Novorossiisk said reports on the fuel spill were being verified.
"The Kapitan Izmail is now afloat in the Black Sea," the office said.
Prosecutors said another vessel, Turkey's dry cargo ship Ziya Kos, which also ran aground near Novorossiisk, is scheduled to be brought afloat this month.
Tens of thousands of birds died in the oil spill. Russian Natural Resources Minister Yury Trutnev estimated the damage from the spill at about $250 million.
Ports have been blamed for a failure to coordinate navigation ahead of the storm. Russian officials said some ship captains could also face negligence charges.
