The mine-sweeper Turbinist had taken part in Russia's "peace enforcement" operations in Georgia.
It entered the Russian naval shipyard in the Crimea, which Russia leases from Ukraine, without incident and was welcomed by locals waving Russian flags and cheering the Black Sea Fleet.
Similar scenes greeted the guided missile corvette Mirazh when it returned to base on Friday.
Ukrainian President Viktor Yushchenko signed a decree this month requiring prior notification from Russia of all movements by naval vessels and aircraft from the country's Black Sea Fleet base in the Crimea.
Ukraine even threatened to refuse Russian vessels entry to the Sevastopol naval base.
The decree is not yet being enforced, and Russia views it as a provocation and is likely to resist any Ukrainian limits on the deployment of its navy.
"I think all issues, including similar provocations, have been discussed under bilateral agreements between Russia and Ukraine on the status of the Black Sea Fleet. We will give a prompt response if anything happens," said Col. Gen. Anatoly Nogovitsyn, the deputy chief of Russia's General Staff.
