The ministry's Zvezda broadcasting service said Russia's Black Sea and Northern Fleets participated in the military exercise.
Various missiles were fired during the drill, including Kalibr cruise missiles and Kinzhal hypersonic air-launched missiles.
More than 30 warships, including the Admiral Grigorovich and Admiral Makarov frigate, one submarine, and more than 40 aircraft, including Tu-95MS strategic bombers, Su-30SM fighters, and Su-24M bombers, participated in the drill.
Two MIG-31K fighters air-launched Kinzhal hypersonic missiles while guided missile destroyers launched Kalibr cruise missiles at targets.
Putin observed much of the exercise aboard the Marshal Ustinov missile cruiser.
"The drills have been held successfully," Admiral Nikolai Yevmenov, commander-in-chief of the Russian Navy, told Putin on Thursday.
The drill comes as the US and Iran were on the verge of war earlier this week. Tensions have simmered down but are still elevated after Iran launched missiles at two US bases in Iraq.