Iraq's Kurdish region, with which Turkey has forged close trade ties, announced this week that it would vote on whether to split from the rest of Iraq and form an independent region.
Turkish Prime Minister Binali Yildirim called the decision "irresponsible", adding that Ankara championed Iraq's territorial integrity.
"We have enough problems in our region. We believe it is not correct to create a new area of conflict," the premier told reporters.
"We believe this is a decision that has been made irresponsibly."
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"We believe that the announcement by the (Iraqi Kurdish region) to hold an independence referendum on September 25... will constitute a grave mistake," it added.
Kurds are touted as the world's largest stateless people, after being denied their own country in the wake of World War I, and are spread between Iraq, Iran, Syria and Turkey.
Turkey has a large Kurdish minority with which the government has been engaged in a multi-decade armed conflict, and Ankara fears that Iraqi Kurdish independence could fuel increased calls for a similar move within its territory.
The solidarity shown in the fight against IS "should be pursued in the post-Daesh period and the issues that concern the future of the country should be tackled with international and constitutional legitimacy," the foreign ministry said, using an alternative Arabic name for Islamic State.
"It is clear that under those extraordinary conditions, a referendum on regions whose status are disputed will be far from reflecting the people's will.
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