"The exercise is in accordance with a plan approved by the Russian Navy," the source said.
RIA Novosti has learned that the exercise is part of a program to ensure security for the 2014 Winter Olympics in Sochi.
The two Russian warships arrived at Novorossiisk after completing a patrol mission in the Black Sea. A high-ranking navy source said a Russian naval group had been in the eastern part of the Black Sea, near Georgia's maritime borders.
The Ukrainian Foreign Ministry had earlier said it reserved the right not to permit the Russian warships back into the country, but Moscow said the Black Sea Fleet would remain in the Crimea under the current agreement until 2017.