Viktor Kravchenko said the joint operation would last up to three months and see NATO and Russian navies jointly patrol the coasts of Mediterranean nations for potential arms smuggling.
Kravchenko said that a similar exercise was successfully completed in December.
"Our main task now is developing joint cooperation while sending inspection crews on board ships," Kravchenko told the news agency.
Russia and NATO have signed a series of cooperation agreements since their bitter standoff in the Cold War.