Moscow and Washington signed the deal on military transit via Russian territory, both overland and by air, on July 6 during President Barack Obama's visit to Russia.
Andrei Nesterenko said the agreement would formally enter into force only after the "legal procedure" was finalized, adding that with regard to Russia that meant its ratification by parliament.
Until then, he said, its implementation would only be provisional.
He also said the United States had not as yet specified "transit parameters or plans."
The official said Moscow operated on the assumption that "Russian-U.S. transit cooperation will become a significant contribution to ensuring security, stabilization and reconstruction of Afghanistan."
The Russian foreign minister previously said Moscow would have the right to inspect U.S. military planes overflying its territory.
Sergei Lavrov also said the U.S. planned to make 4,500 flights to Afghanistan via Russian airspace.
Russia already has bilateral transit deals with Germany, France and Spain, and also signed an agreement with NATO in 2008 on rail transit of non-lethal supplies to Afghanistan.
The U.S.-led International Security Assistance Force (ISAF) has about 64,500 troops in Afghanistan, including 30,000 from the United States, under a UN mandate to give security support to the Afghan government and stop the flow of drugs from the country. There are a total of 62,000 U.S. troops in the country, with that figure set to rise by 6,000.
