Alexander Kolmakov told an informal meeting of the Russia-NATO Council in Vilnius that "the bloc's intention to integrate U.S. national missile defense elements into a NATO security system would have a negative impact on cooperation [with Russia] in this sphere."
The Russian official held a meeting with NATO Secretary General Jaap de Hoop Scheffer in the Lithuanian capital.
Russian Defense Minister Anatoly Serdyukov is also in Vilnius, for the first time since ex-Soviet Lithuania joined the Western military alliance.
NATO officials previously said the bloc could adopt a NATO-Russia cooperation program for 2008.
Russia has been unnerved by NATO's ongoing expansion and Washington's plans to deploy missile defense bases in Central Europe, which it says are needed to deter possible strikes from Iran and other "rogue states."
