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.
"We believe that the announcement by the (Iraqi Kurdish region) to hold an independence referendum on September 25 ... will constitute a grave mistake," the foreign ministry said in a statement, AFP reported.
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.
Ankara had in the past shared worries over the independence plan of Iraqi Kurds, saying it would not be beneficial for Iraq and would cause further instability, the ministry said.
"To preserve Iraq's territorial integrity and political unity is one of Turkey's fundamental Iraq policies," it said.
Ankara also said the major issue faced by Iraq was the fight against the Daesh (also known as ISIL or ISIS) militant group and to rebuild the country after the offensive, which appeared to be reaching a conclusion soon.
The solidarity shown in the fight against ISIL "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 the Arabic name for ISIL.
"It is clear that under those extraordinary conditions, a referendum on regions whose status is disputed will be far from reflecting the people's will."