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"This shows one thing, that this administration (in northern Iraq) has a history with Mossad, they are hand-in-hand together," Erdogan said in a televised speech in Erzurum, eastern Turkey.
Its fierce opposition to the referendum is seen as reflecting anxieties about Turkey's own sizeable Kurdish population.
Neighbouring Iran also opposed the referendum and announced on Saturday that it would be holding joint military exercises with Iraq along the Iraq-Iran border.
In the run up to the vote, Israel emerged as the only state to support the controversial referendum, which only stiffened Iranian and Turkish resistance.
"Are you aware of what you are doing?" Erdogan said, appealing to Iraq-Kurdish leaders. "Only Israel supports you".
Erdogan vowed on Saturday that Iraqi Kurdistan "will pay a price" for the "unacceptable" independence referendum.
"An independent state is not being founded in northern Iraq, but on the contrary a continuously bleeding wound is being opened," he said.
"To ignore this reality benefits neither us, nor our Kurdish brothers in Iraq," he said, urging Iraqi Kurds to "wake up from this dream" of independence.