The Council of the European Union announced Monday that it was authorizing oil imports and related investments in the Syrian oil industry "so as to help the civilian population and support the opposition in that country."
The European Union banned the import of Syrian oil and petroleum products in September 2011.
Bogdanov said the EU decision sidelined the legitimate government in Syria, which he said was in place until a new one is elected by the Syrian people.
"This leads the situation to a deeper deadlock and does not contribute to a political solution of the problems that have accumulated," he was quoted by Russia's state-run news agency RIA Novosti as saying. "So we think this is a counterproductive decision."
Russia is a key ally of the Syrian government of President Bashar Assad. It's said that efforts at the U.N. Security Council to censure Assad's administration lack balance.
The EU decision comes with the stipulation that Syrian transactions can't circumvent existing sanctions against Syria and calls for consultation with the formal opposition movement.
Syria's civil war is in its third year. At least 70,000 people have died and more than 1 million are displaced by conflict.