Russian destroyer Admiral Chabanenko, escorted by two supply ships, the Ivan Bubnov and the SB-406, arrived in Havana Bay on Friday.
Cuban President Raul Castro met on Monday with the deputy commander of the Northern Fleet, Vice Admiral Vladimir Korolev.
The meeting was held "in the atmosphere of friendship and cooperation that characterizes relations between the peoples, governments and armed forces of the two countries," the Granma newspaper said.
Cubans waited in long lines to step on board the Admiral Chabanenko, which was opened to the public on Sunday. Old and young alike waited for hours in line to get on board the destroyer and talk to the Russian sailors. Whole families came to the port to visit the ships and take photographs.
The Russian sailors laid wreaths at a monument to Cuban national hero Jose Marti and the Soviet Internationalist Soldier Memorial, and also visited the newly built Russian Orthodox cathedral, which opened in October.
The group command met with Cuban Navy officials, the mayor of Havana and Russian Embassy staff.
The historic visit to Cuba completed a Caribbean tour by Russian battleships that included stops in Venezuela, Panama and Nicaragua.
Russia announced last year that its Navy had resumed, and would continue to build up, a constant presence throughout the world.