Dmitry Rogozin also accused Georgian President Mikheil Saakashvili of war crimes and a number of Western media of complicity.
"Our relations with the alliance cannot but be affected after Mr. Jaap de Hoop Scheffer failed to say a word about the victims of the attack. Not a single word has been uttered in condemnation of the aggression," he said in an interview with Russia's NTV channel Wednesday.
He said that instead of condemning Georgia's attack on the capital of Tskhinvali on August 8, quite the contrary, Scheffer had started criticizing Russia.
Moscow has said that 1,600 civilians died during the Georgian attack. The majority of residents of Tskhinvali hold Russian passports.
During the subsequent counter operation to expel Georgian troops from the de facto independent republic and to reinforce Russian peacekeepers, Moscow sent some 10,000 troops and several hundred armored vehicles into the area.
Georgia has reported 60 civilian deaths in the city of Gori, near the South Ossetian border. Media sources say that a munitions warehouse was bombed by Russian jets on August 9 and that residential buildings were then hit by subsequent explosions. Russia has strongly denied targeting civilians.
"These statements are hypocritical and irresponsible," Rogozin said, adding that they had come at a time "when we are being subjected to Saakashvili's aggression."
He said Russia's relations with the alliance would now change, although he added that this should not impair global security.
"I hope that this will not affect security as a whole," he said, adding that NATO and "other similar structures no longer measure up to modern security requirements."
The 26 NATO envoys, at a meeting with the Georgian envoy to the alliance on Tuesday, reiterated "in very strong terms" their support for a sovereign, independent Georgia.
NATO Secretary General Jaap de Hoop Scheffer told a news conference the allies "condemned and deplored [Russia's] excessive, disproportionate use of force."
"Georgia is a respected partner and friend and one day Georgia will join NATO," Scheffer said.
Western media reports said on Thursday morning that irregular paramilitary groups tagging behind regular Russian forces had engaged in "looting, burning, murdering and rape" in Georgia.
Russian media earlier reported atrocities by Georgian troops in Tskhinvali, including cases of women and children being "burned alive."
