Russia has repeatedly complained that NATO has too many ships in the Black Sea. Foreign Ministry official Andrei Nesterenko said Tuesday that currently there are two U.S., one Polish, one Spanish and one German ship there.
Russian officials say the United States could have delivered weapons to Georgia under the guise of humanitarian aid.
"We don't understand what American ships are doing on the Georgian shores, but this is a question of taste, it's a decision by our American colleagues," he reportedly said. "The second question is why the humanitarian aid is being delivered on naval vessels armed with the newest rocket systems."
He said Russia's reaction to NATO ships "will be calm, without any sort of hysteria. But of course, there will be an answer," Interfax quoted Putin as saying during a visit to Uzbekistan.
Asked by exactly what measures Russia would take, Putin was quoted as answering "You'll see."
Separately, Russian officials criticized European threats to postpone talks on a partnership deal over the war in Georgia, but the Russian envoy to the EU said he was not surprised that the bloc declined to impose sanctions on Russia.
"We are too interdependent," Vladimir Chizhov told reporters in Moscow. "Russia and the European Union are bound by destiny to be close partners."
EU officials said Monday that unless Russian troops pull back from positions in Georgia, talks on the wide-ranging political and economic agreement would be delayed.
Britain and Eastern European nations held out for a tougher line, but Europe's dependence on Russian oil and natural gas deterred stronger sanctions.
Putin's visit to Uzbekistan only highlighted that dependence: The Russian leader announces a new natural gas pipeline to cross Uzbekistan, strengthening Russian control over Central Asian gas exports to Europe and undermining Western-backed efforts for a rival trans-Caspian route.
Criticizing the EU decision, Russian Foreign Ministry spokesman Andrei Nesterenko said Russia had fulfilled "all of its commitments."
He claimed efforts were under way to rebuild Georgia's armed forces, and said Georgian military forces were behind protests against Russian troops stationed in the country.
"There are active attempts to restore the activity of Georgian troops," he said. "Yesterday, there were rallies and provocations near the town of Kapoleti targeting Russian troops. We believe they were organized by Georgian special services."
Georgian officials could not be immediately reached for comment on the claim.
"Naturally, we cannot agree with a number of biased statements regarding Russia in the final declaration of the summit, including the assertion that our reaction to the Georgian aggression was disproportionate," the Foreign Ministry said in a statement.
"The main thing, however, is that they are in the minority and the majority of EU countries have manifested a responsible approach and confirmed their intention to continue the partnership with Russia," the ministry said.
On Aug. 7, Georgian forces attacked South Ossetia, hoping to retake the province, which broke away from Georgia in the early 1990s. Russian forces repelled the offensive and pushed into Georgia. Both sides signed a cease-fire deal in mid-August, but Russia has ignored its requirement for all forces to return to prewar positions.
Moscow insists the cease-fire accord lets it run checkpoints in security zones of up to 4 miles into Georgian territory.