Russian Chief of the General Staff Nikolai Makarov's comments came at a missile defense conference in Moscow, RIA Novosti reported.
"The placement of new strike weapons in the south and northwest of Russia against [NATO] missile defense components ... is one possible way of incapacitating the European missile defense infrastructure," Makarov said.
He pointed to what he called the "destabilizing nature of the missile defense system" and said "the decision on the pre-emptive use of available weapons will be made during an aggravation of the situation."
Russia had previously warned of strikes on anti-missile sites during war but not pre-emptive strikes.
Nikolai Patrushev, the secretary of Russia's Security Council, said by 2020, the missile defense system could have the ability to intercept Russia's intercontinental ballistic missiles.
The United States and NATO agreed in 2010 to develop the missile defense system. But Russia and the alliance have been at odds over NATO's refusal to guarantee Russia the system wouldn't be aimed at Russia's strategic nuclear deterrent system.
"The refusal to discuss the conditions for providing legal binding guarantees for the deployment system to be not aimed at Russia strengthens our convictions that the real goal of this missile defense system could differ from what is stated," Patrushev said.
Russian Defense Minister Anatoly Serdyukov said Thursday Russia and NATO have not found a "mutually acceptable solution to the missile defense issue, and the situation is at a dead end."
But Alexander Vershbow, NATO's deputy general secretary, said the missile defense system "will be capable of intercepting only a small number of relatively unsophisticated ballistic missiles. It does not have the capability to neutralize Russian deterrence."