The targets were hit with long-range ship-launched missiles, the Russian Ministry of Defense said in a statement, adding that the drones - essentially unmanned boats loaded with explosives - were used by Ukraine to commit terrorist attacks.
The ministry also noted that the missile strike was successful and that all targets have been destroyed.
Last month, Ukrainian forces conducted an attack on the bridge across the Kerch Strait, which links the Crimean Peninsula with Russia's mainland, using such a maritime drone.
Two civilians - a couple - were killed and their teenage daughter was injured in the attack, but the blast failed to deal any serious damage to the bridge itself.
In August, Ukrainian forces also launched an attack using two unmanned boats with explosive payloads against Russian naval vessels in the port of Novorossiysk.