Vassily Nebenzia told a Security Council meeting on threats to international peace that those pardoned by "the authorities of Syrian Kurdistan" included field commanders and "caliphate officials".
One hundred and twenty of those who were granted amnesty entered the ranks of the U.S.-backed SDF umbrella group, according to Nebenzia.
"The fact that such an issue remains virtually unnoticed serves as a testament to a persistent double standard with respect to terrorists," Nebenzia said.
"All those who delivered direct or indirect assistance to ISIL, not to mention the fighters themselves, must be held to account."
Nebenzia was referring to the Islamic State of Iraq and the Levant, another name for Daesh.
The comments come after the U.S. clashed with forces allied to the Bashar al-Assad regime overnight Wednesday in eastern Syria. The Pentagon said the U.S. was supporting SDF forces following "an unprovoked attack by Syrian pro-regime forces".
"Coalition advisors were with the SDF, and this action was taken in self-defense," spokeswoman Dana White told reporters.
Russia is the regime's main ally on the ground in Syria and in the international arena, frequently using its permanent seat on the Security Council to provide Damascus with diplomatic cover within the international community.
Nebenzia slammed the U.S., saying Moscow sees an "intensification" of efforts aimed at "defaming" Russia's efforts to achieve a political settlement.
"As soon as we have some progress on the political front, we see this intensification all the time," he said.
"Russia was invited to Syria by the legitimate government to help defeat the terrorists, and we did so since 2015. The U.S. was never invited. Who is aggressive? You tell me.”