Putin said he doesn't envision a conflict between Russia and the United States, but his blunt remarks reflect a wariness of U.S. intentions.
Putin made the comments at a meeting with students after being asked to comment on suggestions that Russia and other countries relinquish Arctic territory to help protect the environment -- a proposal Putin angrily rejected.
"Experts know quite well that it takes U.S. missiles 15 to 16 minutes to reach Moscow from the Barents Sea," Putin said, referring to the part of the Arctic Ocean near Russia's shore.
The United States seldom comments on the presence of its nuclear-armed submarines, but it is thought that they patrol international waters.
Putin described the Arctic region as essential for Russia's economic and security interests.
"There is a huge amount of mineral resources there, including oil and gas," he said. "It's also very important for our defense capability."
While emphasizing the need for Russia to cooperate with the United States and other countries, Putin added that Moscow has to take into account the U.S. navy presence.
"I proceed from the assumption that we will never engage in a global conflict, particularly with a country like the United States," he said. "Just opposite, we must develop cooperation and partnership, and we have every opportunity for that despite arguments. But the submarines are there, and they do carry missiles."
The Russian military has been restoring a Soviet-era military base on the New Siberian Islands that was shut down after the Soviet collapse. Russian officials said the facility is key for protecting shipping routes that link Europe with the Pacific region across the Arctic Ocean.
In September, a Russian navy squadron led by a nuclear-powered cruiser, visited the archipelago, which occupies a strategic position on the Arctic shipping route.
Russia, the United States, Canada, Denmark and Norway have all been trying to assert jurisdiction over parts of the Arctic, which is believed to hold up to a quarter of the planet's undiscovered oil and gas.
In 2007, Russia staked a symbolic claim to the Arctic seabed by dropping a canister containing the Russian flag on the ocean floor from a small submarine at the North Pole.
It also recently arrested the 30-member crew of a Greenpeace ship following a protest at a Russian oil platform in the Arctic. They were released on bail after spending two months in a Russian jail, but their case is still pending.
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