"Some people want to use militants from al Qaeda ... to accomplish their goals in Syria," Putin said in a speech on Russian television, according to reports by CBS News.
Russia, which sees Syria as its most important ally in the region, has been a staunch opponent of international efforts to oust Syrian President Bashar Assad from power and end the worsening civil war there.
Russian opposition played a key role in the failure of a U.N.-brokered peace plan in March, spearheaded by former U.N. Secretary General Kofi Annan.
Moscow has also sent special forces and Marine units into Syria, to conduct anti-terrorism operations in support of the Assad regime.
Over the past 18 months, anti-government forces have been locked in brutal, street-to-street fighting with Syrian troops and paramilitary forces loyal to the Assad regime.
While rebel forces have managed to carve out strongholds in the northern part of the country, Assad's forces have managed to push their way into the region. Using heavy artillery and superior air power, Assad's forces have been bludgeoning rebel positions in and around the northern Syrian city of Aleppo.
Al Qaeda militants based in Iraq have also begun to flood the country, looking to take advantage of the conflict and establish a new terror cell in Syria, according to Defense Department officials.
In August, rebel commanders battling Assad's forces in northern Syria said they would consider aligning themselves with the throngs of al Qaeda fighters streaming into the country.
"We don't want al-Qaeda here, but if nobody else helps us, we will make an alliance with them," Abu Ammar, a rebel commander stationed in Aleppo, told Reuters at the time.
"And you can bet if Al-Qaeda comes here ... the city will become their base within three months," he said.
Rebel leaders have pleaded with the United States and its allies to establish a no-fly zone in northern Syria, patrolled by American air power, as a way to counter Assad's blistering air assaults in Aleppo and elsewhere.
Anti-government forces have also repeated calls for the United States and its allies to begin funneling arms to rebel forces.
But DOD and the White House have held off on efforts to supply Syrian fighters with weapons directly, amid concerns that if heavy weapons are funneled into Syria, it’s possible those arms could later be turned against American or allied troops by al Qaeda fighters.
That said, the Pentagon continues to argue that Al Qaeda militants have not infiltrated the rebels' ranks, but that scenario could change quickly if rebel leaders decide to open up their forces to the terror group.