Karasin was meeting with his Ukrainian counterpart, First Deputy Foreign Minister Yuriy Kostenko.
"The Russian side stressed the unacceptable nature of Ukraine's unilateral actions concerning Russia's Black Sea fleet base in Ukraine," the Foreign Ministry said in a statement.
Frequent disputes have flared up between Russia and Ukraine over the lease of naval facilities on the Crimean peninsula.
Russia's Black Sea Fleet uses the Sevastopol base under an agreement signed in 1997. Ukrainian President Viktor Yushchenko recently decided not to extend the lease beyond May 28, 2017.
In early June, Russia's lower house of parliament adopted a resolution saying the Russian-Ukrainian cooperation treaty could be denounced if Ukraine joins NATO.
Ukraine's pro-Western leadership has been pursuing NATO membership since the 2004 election of President Viktor Yushchenko. Ukraine failed to secure an agreement on a NATO Membership Action Plan, a key step toward joining the alliance, at the organization's summit in April, but was told the decision would be reviewed in December.
