Baluyevsky criticised plans by the US to deploy 10 interceptor missiles in Poland and a radar in the Czech Republic by 2012, as part of the missile defence shield.
Russian missiles could be triggered if the country’s automated defense system mistook US interceptors for a ballistic missile aimed at Russia, he warned.
Baluyevsky disputed Washington's claims that the US plan was intended as a guard against a potential missile threat from Iran, saying instead it was an attack on Russia.
"If we assume that Iran does try to launch a missile against the United States... then interceptor missiles from Poland would fly in the direction of Russia," he said.
Sergei Kislyak, Russia's deputy foreign minister, said despite diplomatic efforts by the two countries, consultations over the proposed shield had been "disappointing".
On Wednesday, Russia withdrew from the Conventional Forces in Europe (CFE) treaty, a key Cold War agreement that limited the stationing of troops and heavy weapons in Europe.
Russia said it pulled out of the CFE because of the 26-nation Nato alliance’s failure to ratify a revised 1999 version of the treaty.
Nato countries have refused to do this until Moscow withdraws its troops from the former Soviet republics of Georgia and Moldova.
Mosocow also cited Washington's refusal to back down over the planned missile shield as a key factor in its decision to leave the treaty.
Russia's withdrawal raised protest from the US as well as Nato which called the move "deplorable".
Baluyevsky's comments came a day after Alexander Lukashenko, the Belarussian president, said he would side with Moscow in the missile shield dispute.
Last month a Russian general in charge of the country's missile and artillery forces said Russia could counter US plans by deploying missiles in Belarus, which is located between Russia and Poland.