Speaking in a live TV interview, Yildirim said the Kurdish Regional Government (KRG) independence referendum in northern Iraq was illegitimate and its results would be null and void.
"From now on, we will directly speak to Iraq's central government and decide accordingly," the Turkish premier added.
"[The vote] will not contribute to regional peace and stability, but it will increase already-existing tension and problems," he said.
Yildirim said the "insistence” on the vote had, in a sense, created an “environment for conflict".
He said Turkey would have more dialogue with Baghdad over "all border gates and airports and energy issues".
Slated to be held on Monday, the non-binding referendum will see Iraqis in KRG-controlled areas -- and in a handful of territories disputed between Erbil and Baghdad -- vote on whether or not to declare independence.
Along with Baghdad, Turkey, the U.S. and Iran, the UN has spoken out against the referendum, saying it will distract from the ongoing fight against Daesh and further destabilize the region.
Iraq’s central government has even threatened to intervene militarily if the vote leads to violence.
'Pain and tears'
The referendum decision "was taken without taking into consideration the future of people from all ethnicities," Turkish premier said.
"It will not bring a better future for Turks, Arabs, Kurds and Turkmens, but will bring more pain and tears," he insisted.
Stressing that Turkey did not regard the referendum issue in a sectarian way, Yildirim said:
"No one should ever think that we are against Kurds. We have people from all ethnicities."
However, he also said his country would not be indifferent to actions against Turkmens in the region.
About threats to Turkey’s national security, the prime minister said "no new entity on Turkey's southern borders is acceptable".
However, he also moved to assure the public that Turkey "is not involved in a war," describing recent Turkish military drills near the Iraqi border as a precaution.
The prime minister also announced that President Recep Tayyip Erdogan would visit Iran on Oct. 4 when the countries will discuss regional matters, including the KRG independence vote.