Putin arrived in Athens on a two-day visit yesterday and emerged from talks with the Greek government to lash the United States and NATO allies, also accusing them of stifling trade and energy cooperation with Russia.
Earlier this month, the US program was declared operation at a site in Romania, drawing an angry reaction from Russia.
NATO says the system is purely defensive and a response to a growing capability of ballistic missiles globally.
"Of course it's a threat to us. It can easily be modified to have an aggressive capability ... We are obliged to take action in response to guarantee our security," he said, without elaborating.
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Putin has made only a handful of visits to EU countries since sanctions were imposed on Moscow two years ago in response to the Ukraine crisis and Russia's annexation of Crimea following an internationally disputed referendum.
"The issue of Crimea is over forever, based on the will of the people who live there. Russia will never negotiate on this issue," Putin said.
Russia is one of Greece's main trading partners, but business has been hit by the sanctions and a drop in commodity prices.
Greece is also keen to reverse a slump in tourist arrivals from Russia last year, and attract interest from Russian companies in the planned privatisation of rail and other transport services.
Alexis Tsipras, the Greek prime minister, noted that Putin's visit comes just days after Athens reached a deal with eurozone bailout creditors to continue rescue loans, under a deal that expands power of a state privatization committee.
Putin travelled to Greece with Russian Foreign Minister Sergey Lavrov and top executives from state oil and gas companies. Amid heavy security at Athens Airport, air force F-16s buzzed overhead as part of a welcoming ceremony.
"This will be the first time Putin has visited an EU country in the past six months and Russia-EU relations will be definitely on the agenda," said Alexander Kokcharov of the U.S.-based IHS Country Risk group.