Speaking at a news conference with Ukrainian President Viktor Yushchenko, Putin said Ukraine's aspirations to join NATO would restrict its sovereignty.
"That raises the question for Russia of the need for retaliatory actions," Putin said.
"It is frightening not only to talk about this, but even to think that, in response to such deployments ... and one can't theoretically exclude these deployments, Russia would have to point its warheads at Ukraine," he said.
Yushchenko responded by saying that Ukraine has the right to form its own foreign and defense policies, and noted that the Ukrainian constitution does not allow for the deployment of foreign bases on its territory.
"You understand well that everything Ukraine does in this direction is not in any way directed at any third country, including Russia," he said.
Putin and Yushchenko said they would continue talks about the legal status of Russia's Black Sea Fleet, which is stationed on Ukraine's Crimean peninsula. The two countries signed an agreement in 1997 allowing the fleet there for a rent of $93 million per year. Ukraine has tried to increase the price.