The referendum today was proceeding peacefully but there were fears of potential unrest, especially after lawmakers in Baghdad demanded that troops be sent to disputed areas where voting was taking place.
Guterres again called on Baghdad and the Kurdistan regional authorities to resolve differences through dialogue and compromise.
The UN chief also told Iraqi Kurd authorities to ensure that the work of the UN mission in Iraq "will be allowed to continue unhindered."
More than 5.3 million people were registered to vote in the referendum, which has been opposed by the United States and major regional powers.
Guterres said he was "concerned about the potentially destabilizing effects of today's referendum in the Kurdistan region of Iraq," in a statement from his spokesman.
The UN chief added that he "respects the sovereignty, territorial integrity and unity of Iraq" and considers that all differences "should be resolved through "structured dialogue and constructive compromise.
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