"As the alliance's leadership has ignored the important peacekeeping role of Russia in the Caucasus and South Ossetia we believe it is expedient to suspend all peacekeeping operations between Russia and NATO for at least six months," Dmitry Rogozin said.
However, the diplomat stressed that Russia was not opting out of political dialogue with NATO.
Georgia attacked South Ossetia on August 8 in an attempt to take back the separatist republic, which split from Tbilisi in the early 1990s.
Most people living in South Ossetia have Russian citizenship and Moscow subsequently launched an operation to "force Georgia to accept peace." The operation was concluded on August 12.
Russia's president signed two decrees Tuesday recognizing South Ossetia and another separatist region, Abkhazia, as independent states and called on other countries to follow suit.
"This is not an easy decision, but it is the only way to protect people's lives," Dmitry Medvedev said in a televised address.
Both houses of Russia's parliament voted unanimously on Monday on a resolution asking the Russian president to recognize the independence of Abkhazia and South Ossetia, following requests from the leaders of both breakaway republics.
The move will further worsen Russia's relations with the West, already strained over Moscow's military actions in Georgia.
Rogozin also said Russia had decided to delay sending its chief military representative to NATO.
"For the time being we can see no necessity and possibility of sending Russia's chief military representative to Brussels," he said.
The Russian envoy himself was recalled from Brussels "for consultations" after NATO froze contacts through the Russia-NATO Council on August 19, accusing Moscow of disproportionate use of force against Georgia. Russia's Defense Ministry later said it was suspending all cooperation with the military alliance.
Rogozin said Russia would suspend its participation in NATO's Partnership for Peace program. "I see no possibility for maintaining the project. It will be suspended," he said, although he added that Moscow would continue to participate in the Russia-NATO Council.
The Russian envoy said Russia was proposing that visits to the country by NATO leadership and naval ships, as well as joint exercises, be postponed.
"We believe that visits by high-level representatives of NATO military leaders to the Russian Federation should be postponed. In addition, we intend to suspend the practice of visits to Russian ports by NATO warships, permanent military formations..., as well as suspend participation of Russian troops and forces in joint exercises," Rogozin told journalists.
But he said Russia was not planning to cease its cooperation with NATO on Afghanistan.
"We are working from the position that the situation in Afghanistan is a common problem. The Taliban have been extremely active of late," he told reporters.
Rogozin said Russia had no plans to quarrel with NATO and was looking to restore a normal relationship with the military alliance.
"We will struggle for the restoration of peace and calm - the restoration, eventually, of a normal partnership with our colleagues," he said.