He believes that the ten missile interceptors and radar base to be stationed in Poland and the Czech Republic are aimed against Russia.
"For the first time elements of the US strategic nuclear system are appearing on the European continent," Mr Putin was quoted as saying by the Reuters news agency.
"This element dramatically changes the security situation in Europe. We do not understand… what is happening in Europe now that requires such aggressive actions. We see no arguments for deploying the missile shield in Europe."
Mr Putin rejected claims that the missile system was targeting threats from terrorists based in the Middle East. He preferred to point out that the warheads' range stretches as far as the Ural mountains, marking the farthest boundaries of European Russia.
The Russian president's comments come one day after he threatened to withdraw from the 1990 conventional forces in Europe (CFE) treaty.
That decision, which he said was motivated by the eastward expansion of Nato's theatres of operations, has been criticised by the US and UK governments, as well as by Nato itself.
Click here to run an energy price comparison, and see if you could be paying less for your gas and electricity.