Three dry freighters containing sulphur and an oil tanker with 4,000 metric tonnes of fuel oil on board went down in the northern part of the Black Sea.
The bodies of three sailors have been found, and at least eight other sailors are still missing, according to the ministry.
"Three teams have started an operation to contain the oil spill caused by the Volgoneft-139 tanker sinking [in the Kerch Strait]," ministry Spokesman Viktor Beltsov said.
During the storm, at least four barges ran adrift in the Kerch Strait off the Russian coast near Ukraine, and in the Black Sea. When the tanker was split in two, 2,000 metric tonnes of fuel oil and about 6,800 metric tonnes of sulphur spilled into the sea, in one of Russia's worst environmental disasters in recent years.
Oleg Mitvol, deputy head of Russia's environmental regulator, said the sinking of the ships in the Kerch Strait was a serious disaster, and it would take more than a month to clear up the environmental pollution.
Meanwhile, environment watchdog Greenpeace Monday warned that the fuel oil spill between the Black and Azov Seas could destroy rare fauna in those waters.
According to Vladimir Chuprov, head of the energy department at Greenpeace, Russia, heavy elements of fuel oil will settle on the seabed and cause hydrocarbons to permeate the Sea of Azov following the oil spill. "This will lead to a shortage of oxygen in the water, and the unique fauna will suffer greatly," he said.
Greenpeace said the sulphur spill posed a lesser threat than the fuel oil. Alexei Kiselyov, coordinator of the environmental group's toxic substances division, said the sulphur consignment had been transported in containers and could be easily lifted from the seabed.
"Even if one of the containers burst, it will not be particularly dangerous because there is nothing sulphur can react with in water," he said.