At least 100 people were killed, allegedly by fighters loyal to Syrian President Bashar Assad, last week in the coastal towns of Baida and Banias. Davutoglu said the attacks were was part of a broader campaign to create a safe haven for Alawites in western Syrian.
Sunnis make up the majority of the Syrian population. Assad is an Alawite, a division within the Shiite minority.
"In the Banias massacre, we are concerned over this fact: If it is impossible to control the entire country, the new strategy involves ethnically cleansing some areas and trying to hold on to this territory," Davutoglu told Turkish daily newspaper Hurriyet.
Davutoglu said the civil war in Syria has entered a new stage where Allawites are cleansing the area of Sunnis to create a corridor to Lebanon.
Davutoglu said this week the latest campaign was part of Assad's so-called Plan B. He compared the alleged massacre to the massacre at Srebrenica, a 1995 assault by Serbian forces that left more than 8,000 Muslim teenagers and men dead.
NATO forces have deployed Patriot missiles to protect Turkish borders.
The Turkish newspaper said thousands of Sunnis have fled the region out of fear of a massacre, something the Turkish prime minister said Assad's regime would "definitely" regret.