"Our response will be calm, not hysterical, but there will definitely be a response," Putin said.
NATO sent a number of ships, including U.S. warships, into the Black Sea after Russia completed its operation "to force Georgia to peace" on August 12.
The operation came as a response to Georgia's attack on South Ossetia on August 8.
The U.S. has delivered millions of dollars of what it says is humanitarian aid to its ally Georgia. Russia has however questioned the nature of the deliveries.
"If the talk is about humanitarian aid to one of the parties to the conflict, I believe that...it should go to the victims of aggression, that is to South Ossetia," Putin said, adding that it was unclear why warships were needed to carry humanitarian aid.
Deputy Chief of the Russian General Staff Colonel General Anatoly Nogovitsyn also said on Tuesday that Russia was concerned over the presence of the five NATO warships in the Black Sea.
Moscow recognized South Ossetia and Abkhazia as independent states on August 26, and Putin said it was not that significant for Russia that no other country had so far followed suit. Western countries have condemned the move as an "irresponsible decision."
Russia said that the decision was taken to protect the region following Georgia's attack on South Ossetia during which hundreds of civilians were killed and thousands forced to flee the devastated region.
Abkhaz President Sergei Bagapsh told journalists Tuesday that he hoped the republic would be recognized by another 10-11 states.
The Russian premier also said there were no Russian troops in Georgia, including in Poti. "There are no Russian troops on Georgian soil - there are only peacekeeping forces," Putin said.
A number of Western countries have accused Russia of failing to withdraw troops from Georgia in line with a peace plan agreed on by Russian President Dmitry Medvedev and his French counterpart Nicolas Sarkozy. Moscow has repeatedly said it had withdrawn all troops from the area by August 22.
Putin also said the joint statement signed by European Union leaders at Monday's summit showed that relations with Europe would develop despite the Georgia conflict.
EU leaders, meeting in Brussels to discuss the situation in Georgia, condemned Russia's actions in the recent conflict, but stopped short of sanctions.
"Thank God, common sense prevailed. We do not see any extreme conclusions or proposals, and this is very good," the Russian premier said. "We have a foundation to continue dialogue with our European partners."
Putin complained that EU leaders failed to condemn Georgia's aggression, but noted that French President Nicolas Sarkozy had spoken of "the [Mikheil] Saakashvili regime" at a press conference.
"No one talks of 'the Sarkozy regime' about the French political system, or 'the Merkel regime' about Germany, and no one says 'the Brown regime' about Britain, but regarding Georgia 'the Saakashvili regime' did not sound unusual," Putin said.
"This means [Georgia] is not a democratic state, and there is a regime of personal power ... There is and can be nothing democratic in its nature," he said, adding that this provides "certain points of mutual understanding" for Russia and the EU that "can be put forward as a foundation for further dialogue."
President Medvedev said on Tuesday he regrets the EU does not have a "full understanding" of Russia's actions to repel Georgian aggression. "This is sad, but not fatal, because everything in this world is changing," he told Euronews.