Anatoly Serdyukov and Franz Josef Jung are meeting in Moscow as part of the German minister's current visit to Russia.
"One of the issues on the meeting agenda is the transit of military equipment and supplies for the German military contingent in Afghanistan via Russia, including by rail," the source said.
Russia's Foreign Ministry said in November last year that Moscow had given Germany the go ahead to use its rail network to transport weapons, military equipment and supplies to Afghanistan.
The top Russian military official also said he discussed with his German counterpart issues concerning memorials for Soviet and German soldiers, who perished in WWII, joint military exercises and tackling piracy.
The German defense minister thanked Russia for the support given to its German military contingent, which "was initially provided by air and now by rail."
NATO's International Security Assistance Force (ISAF) has about 53,000 troops in Afghanistan under a UN mandate to help support security for the Afghan government and stop the flow of drugs from the country.
Despite recent deterioration in relations with NATO, Russia continues to support the military alliance's operations in Afghanistan, and has said it shares NATO's concerns over the worsening security situation in the country.