Washington has asked Poland and the Czech Republic to host components of the system.
"The American decision is presented in such a way that is disrespectful to its partners in the EU and even in relation to other members of NATO," Lavrov said in an address to the State Duma, the lower house of Russia's parliament.
Lavrov's comments followed a warning from German Foreign Minister Frank-Walter Steinmeier that the U.S. plans could lead to a new arms race on the continent. Berlin has also said that NATO should be consulted about the U.S. plans.
Warning on Kosovo
In a speech that spanned most of Moscow's main foreign-policy concerns, Lavrov also reiterated Moscow's warning that it would reject a United Nations plan for Kosovo if it ignored Serbia's interests.
The plan, drafted by UN envoy Martti Ahtisaari, would grant Kosovo internationally supervised statehood. Serbia opposes the plan and Lavrov indicated that Russia might veto it in the UN Security Council.
Lavrov denied, however, that Russia was planning to use the Kosovo issue to further Moscow's interests in Georgia's South Ossetia and Abkhazia regions.
Russian President Vladimir Putin has suggested that independence for Kosovo could set a precedent in the two pro-Moscow breakaway regions.
"We are not rubbing our hands in anticipation of Kosovo breaking away from Serbia so we can do the same to these republics," Lavrov said. "We are not, and perhaps it would be wrong to take such a position. Our aim is to develop comprehensive relations in all areas with these republics. There are our citizens in those regions and we care about their social problems."
In an apparent reference to the United States, Lavrov also criticized meddling in the Commonwealth of Independent States (CIS) by outside powers.
"In recent years, there has been a considerable increase in the presence and activities on the CIS territory of forces from outside the region," Lavrov said.
"Somebody is trying to draw Russia into some sort of deep rivalry, if not outright confrontation, in the region. We do not intend to succumb to provocation. We are building transparent, understandable relations with CIS states based on sober economic calculations," he added.
On the subject of Iran, Lavrov said Russia will not support "excessive sanctions" against Iran in the UN Security Council. The United States is pushing for the Security Council to impose tougher sanctions against Iran if it refuses to stop enriching uranium.
Lavrov said Russia's plans to help Iran build the Bushehr nuclear power plant is not a threat to the nuclear nonproliferation regime.
"What is being done [at the Bushehr nuclear power plant in Iran] does not present any threat from the point of view of the proliferation of weapons of mass destruction, in this case nuclear weapons. On the contrary, it is a model of how the nonproliferation regime works."