Censor.NET reports citing The Hurriyet Daily News.
Erdoğan also accused Armenia of not sticking to a truce with Turkey's ally Azerbaijan in the territory.
"I hope the steps taken by Azerbaijan to end fighting will be imitated by Armenia, but this is not the case right now," said Erdogan about the territory, which was captured from Azerbaijan by Armenian separatists in an early 1990s war.
Erdoğan earlier expressed his support for Azerbaijan and declared that "Karabakh will one day return to its original owner."
"Russia says that Turkey is taking sides. If we are looking for someone who is taking sides, it is Russia," Erdoğan said.
"Russia likes taking sides; it has done so in Ukraine, Georgia and today in Syria," he added.
Russia stands accused of fuelling separatist tensions and wars in both eastern Ukraineand the Georgian breakaway regions of South Ossetia and Abkhazia.
It is also accused of siding with the Syrian government by targeting opposition forces with air strikes rather than the Islamic State of Iraq and the Levant (ISIL).