"If (Massud) Barzani and the Kurdish Regional Government do not go back on this mistake as soon as possible, they will go down in history with the shame of having dragged the region into an ethnic and sectarian war," Erdogan said in a televised speech.
Iraq's Kurds on Monday voted in a historic independence referendum despite fierce opposition from Baghdad and neighbouring countries Iran and Turkey.
Turnout was 72 per cent, with 3.3 million of the 4.58 million registered voters taking part, election commission spokesman Shirwan Zirar said late Monday.
Erdogan described the vote as a "treason to our country" since it had come at a time of good relations between Ankara and its neighbour the KRG.
He urged Barzani to "give up on an adventure which can only have a dark end.