Iraq's Kurds overwhelmingly backed independence in Monday's referendum, defying neighbouring countries which fear the vote could fuel Kurdish separatism within their own borders and lead to fresh conflict.
"They are not forming an independent state, they are opening a wound in the region to twist the knife in," Erdogan told members of his ruling AK Party in the eastern Turkish city of Erzurum.
Erdogan has built strong commercial ties with Kurdish authorities in northern Iraq, which pump hundreds of thousands of barrels of oil daily through Turkey for export to world markets.
"We don't regret what we did in the past. But since the conditions are changed and the Kurdish Regional Government, to which we provided all support, took steps against us, it would pay the price," he said.
Turkey has repeatedly threatened to impose economic sanction, effectively cutting their main access to international markets, and has held joint military exercises with Iraqi troops on the border.
However, after Erdogan said that Iraqi Kurds would go hungry if Ankara halted the cross-border flow of trucks and oil, it has said that any measures it took would not target civilians and instead focus on those who organised the referendum.
Iraq's Defence Ministry said on Friday it plans to take control of the borders of the autonomous Kurdistan region in coordination with Iran and Turkey.
Turkish Prime Minister Bin Yildirim, speaking on Saturday, did not refer specifically to those plans, but said Ankara would no longer deal with Kurdish authorities in Erbil.
"From now on, our relationships with the region will be conducted with the central government, Baghdad," he said. "As Iran, Iraq and Turkey, we work to ensure the games being played in the region will fail."