"We're analyzing where the strikes are going every morning. The vast majority are not against IS at all," he said, speaking exclusively to The Sun.
"Our evidence indicates they are dropping unguided munitions in civilian areas, killing civilians, and they are dropping them against the free Syrian forces fighting Assad."
"He's shoring up Assad and perpetuating the suffering," he said.
Fallon's outburst is the strongest attack yet by a Government official on Russia's entry into the civil war.
And he conceded the Kremlin's surprise actions have made the West's plans for a no-fly zone or safe haven to protect fleeing refugees a lot harder to implement.
Fallon also revealed he has held face-to-face talks with the King of Jordan about setting up a no-fly zone in southern Syria.
But he denied Putin has left Europe and the U.S. looking weak by acting before them.
"I don't accept he has outmaneuvered us. He has complicated the situation in Syria. But we're not powerless," Fallon said.
He insisted Putin's actions won't stop the Government from widening RAF assaults on IS in Syria.
And he said progress has been made in talks with backbench Labour MPs to win their support for such strikes.
It would be "morally wrong" not to go after IS in Syria, he said, adding: "We can't leave it to French and Australian, American aircraft to keep our own British streets safe."
He also ripped into MPs and peace groups who attacked the drone strikes that killed British jihadi fighters Reyaad Khan and Ruhul Amin in August.
Fallon authorized those raids from his office on the MoD's fifth floor, where he spoke to The Sun on Friday.
Fallon said: "A group called Reprieve was moaning about this."
"I don't remember Reprieve saying anything about 30 British citizens being slaughtered on a Tunisian beach," he said.
