Yerzhan Ashikbayev said only the land transit of civilian cargoes for the U.S. contingent in Afghanistan had been allowed. He also said that their "technical and commercial parameters" had yet to be specified.
Moscow said on Friday it would allow the transit of non-military supplies for U.S. troops in Afghanistan as soon as Washington provided Moscow with cargo specifications.
Several NATO nations, including France, Germany and Canada, already transport so-called non-lethal supplies to their contingents in Afghanistan via Russia under bilateral agreements. Washington is expected to follow suit after striking a similar deal with Moscow in mid-January.
Due to worsening security on the main land route from Pakistan and the expected closure of a U.S. airbase in Kyrgyzstan, NATO is seeking alternative routes to supply the U.S.-led International Security Assistance Force (ISAF) in Afghanistan.
There are 62,000 foreign troops in Afghanistan, and new U.S. President Barrack Obama has pledged to deploy another 30,000 U.S. military personnel to the war-ravaged country.
Despite the recent deterioration in relations with NATO, Russia has continued to support the military alliance's operations in Afghanistan.