Speaking to Turkish reporters on his plane as he returned from the UN General Assembly in New York, Davutoglu rejected Moscow's insistence that its campaign of air strikes launched this week was aimed at Islamic State (IS) extremists.
"The outcome is very worrisome," Davutoglu was quoted as saying in several Turkish dailies including Hurriyet and Milliyet.
"The operation has been entirely against positions of the Free Syrian Army (FSA)," said Davutoglu, referring to the main moderate armed group fighting Assad and which Turkey supports.
"This is clearly supporting the Syrian regime which is on the verge of collapse," he added. "I don't think it will be of benefit to destroy the moderate opposition," Davutoglu added.
Russia and Turkey have been at odds over the Syrian conflict since the unrest erupted in 2011, with Ankara calling for the ousting of Assad but Moscow one of his most important supporters.
Turkey was initially wary of taking tough action against the IS militants who have captured swathes of Syria.
But Ankara is now seen as a full member of the US-led coalition against the extremists and has carried out its own air strikes on their positions inside Syria.
Davutoglu complained that the positions hit by Russia in its Syria air campaign would "benefit IS".
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ