It hopes to build a radar station in the Czech Republic and to site interceptors in Poland. But Moscow insists that the installation of US missiles in countries close to its western border would change the strategic balance in Europe.
Lt Gen Vladimir Popovkin, commander of Russia's space forces, said Moscow would interpret the move as a military threat.
"Our analysis shows that the deployment of a radar station in the Czech Republic and a counter-missile position in Poland are an obvious threat to us.
"It is very doubtful that elements of the national US missile defence system in eastern Europe were aimed at Iranian missiles, as has been stated," he said.
Col. Gen. Vladimir Popovkin, chief of the Space Forces branch of the military, which is responsible for missile detection, spoke two days after the Czech prime minister said the United States had asked to position a radar base in his country that would be part of the global missile defense system.
"Our analysis shows that that the placement of a radar station in the Czech Republic and an anti-missile position in Poland would create a clear threat for Russia," the RIA-Novosti and Interfax news agencies quoted him as saying.