Speaking to foreign reporters at his Istanbul offices in the Ottoman-era Dolmabahce Palace on the Bosphorus, Davutoglu said he was nonetheless ready to work with Moscow to prevent a repeat of the November 24 incident.
"Russia is trying to make ethnic cleansing in the northern Latakia (region) to force (out) all Turkmen and Sunni populations who do not have good relations with the (Syrian) regime," Davutoglu told foreign reporters in Istanbul.
He said Russia wanted to purge the northwestern Syrian region of unwanted elements to ensure the security of its air and naval bases in Syria.
"They want to expel, they want to ethnically cleanse this area so that regime and Russian bases in Latakia and Tartus are protected," he said.
"They don't want to see any Sunni Arab or Turkmen population in that part of Syria. That is the purpose," Davutoglu said.
The region is a stronghold of Alawite Muslims loyal to the Kremlin's ally President Bashar al-Assad who Ankara wants to see ousted.
- 'IS benefitting' -
Davutoglu also said that Russia's military strikes in Syria, which began in late September, were "strengthening" IS jihadists by targeting moderate forces opposing Assad, especially around Azaz in northern Syria.
"Unfortunately the Russian operations are not helping to clean this region from Daesh," he said, using the government's preferred acronym for IS.
He said Russia was bombing Azaz "which is a stronghold of moderate opposition against Daesh".
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"They are bombing Azaz to weaken the opposition, who is fighting Daesh. It means they (Russia) are strengthening Daesh.
"Who is benefitting from this? Daesh. Not even the regime. Daesh."
Davutoglu said just 10 percent of Russia's strikes in Syria targeted IS whereas 90 percent targeted "moderate forces" opposed both to Assad and the jihadists.
He said the Russian actions were affecting plans for joint operations with the US and moderate Syrian rebels to secure the border from jihadists.
"Of course this this is a new situation. We have to assess it with allies about what to do next and when."
- 'Repeat of similar incidents' -
The shooting-down of the Russian Su-24 warplane by Turkish fighter jets has led to a crisis in ties between Moscow and Ankara unprecedented since the Cold War.
Moscow insists the plane never strayed from Syrian airspace but Turkey says it was shot down after repeatedly violating its airspace.
Davutoglu said he was "ready to work" with Russia to prevent a repeat of the incident, warning such confrontations risked happening again without proper coordination.
"If everyone acts on his own then will always be these types of unnecessary, unintentional confrontations."
He said it was dangerous for two coalitions -- Russia and the Syrian regime on one side and the US and its allies on the other -- to be working in the same area.
"What did we learn from this? Two coalition air forces cannot make operations on the same ground at the same time without coordination," Davutoglu said.