"The train has left the Riga port heading for transit to Afghanistan through Russian territory," the source said.
The Russian Foreign Ministry said on Monday that a consignment of U.S. non-military cargos was being prepared in the Latvian capital of Riga for transit to Afghanistan via Russia, and would soon be dispatched.
Russia and NATO signed a framework agreement on the transit of non-military cargos in April 2008, and a subsequent Russia-U.S. deal was signed in January.
Due to worsening security on the main land route from Pakistan and the expected closure of a U.S. airbase in Kyrgyzstan, NATO has to rely on alternative routes to supply the U.S.-dominated International Security Assistance Force (ISAF) in Afghanistan.
There are over 60,000 foreign troops in Afghanistan, more than half of them from the United States, and President Barack Obama has recently ordered another 17,000 U.S. soldiers 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, fearing the worsening security situation and the steadily growing opium production in the country.
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.
The "northern corridor" for U.S. transshipments through Russia would likely cross into Kazakhstan and then Uzbekistan before entering northern Afghanistan.
U.S. officials earlier said 20 to 30 trainloads a week could go from Latvia to Afghanistan if the route is a success.