Russia is building Turkey's first nuclear power plant in Akkuyu on the shores of the Mediterranean, a controversial USD 20 billion project aimed at improving its energy self sufficiency.
Turkey is also one of the top importers of Russian gas and had joined forces with Moscow in a major project to build a new gas pipeline underneath the Black Sea.
But speaking to Turkish reporters en route to Japan, Erdogan warned Moscow such cooperation was at risk due to its bombing of Syria and violations of Turkish airspace.
"Russia has already invested $3 billion in this project. In this case, it's Russia who should act with more prudence."
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He added that energy-poor Turkey was even capable of going elsewhere for its natural gas supplies.
"We are a number one consumer of Russian natural gas. If necessary, Turkey can take its natural gas from many other different places," he added.
"We are saddened that Russia is acting in a way that could provoke the loss" of its economic interests in Turkey, he said.
Ankara, a NATO member, is furious over Russia's air campaign in Syria to prop up the regime of President Bashar al-Assad, who Turkey wants to see ousted.
Meanwhile, Russian warplanes have twice violated Turkish airspace.
On a visit to Ankara in December 2014, Putin announced that Turkey and Russia would team up to build a new TurkStream pipeline to pump Russian gas to Europe underneath the Black Sea and avoiding Ukraine.
But TurkStream appears to have become a casualty of the latest tensions, with Russian gas giant Gazprom yesterday saying that the project would be delayed.