Yildirim spoke on Thursday, a day after Iraqi Prime Minister Haider Al-Abadi visited Turkey to discuss possible steps against the Iraqi Kurdish leaders.
Yildirim said the two sides discussed the possible opening of a border gate between Iraq and Turkey that would bypass the Iraqi Kurdish region.
Yildirim's remarks came as Turkey's Foreign Minister Mevlut Cavusoglu said the Iraqi Kurdish offer for last month's referendum on independence to be frozen is "not enough," instead urging the Irbil government to cancel the vote.
"It is an important move that the northern Iraqi administration takes a step back but it is not enough. This referendum should be cancelled," Cavusoglu told a press conference in Ankara.
Turkey, along with Baghdad and other neighboring countries, strongly opposed the Iraqi Kurds' non-binding vote on independence.
The Kurdistan Regional Government, led by Massud Barzani, said on Wednesday it would propose to the federal government "the freezing of the results of the referendum... and the start of an open dialogue" on the basis of the constitution.
However, Iraqi Prime Minister Haider Al-Abadi said Baghdad would only accept the annulment of the referendum.
The Kurdish offer came after Iraq seized large areas of territory that Kurdish forces had captured over the years beyond the borders of the autonomous region.
Yildirim appeared to dismiss the impact of the offer.
"The northern Iraq administration can take whatever decision it wants from now on, it is obvious the decisions will not produce a result that would compensate for the damage," he said at a press conference in Ankara with Somali Prime Minister Hassan Ali Khaire.
Al-Abadi was in Ankara on Wednesday where he met Yildirim and President Recep Tayyip Erdogan to discuss the vote among other regional issues.
The leaders promised to strengthen cooperation as ties between their two countries as ties warm over their shared opposition to the vote.
President Recep Tayyip Erdogan on Wednesday offered Turkish support for the reopening of a pipeline that would allow the central Iraqi government to export oil directly to Turkey, bypassing the Iraqi Kurdish region.
The spokesman for the US-led coalition said the fighting between Iraqi government and Kurdish forces has impeded the movement of coalition military equipment in both Iraq and Syria, negatively impacting the campaign against Daesh.
The US uses the border between Iraq's Kurdish region and Syria to access its Syrian allies, the Kurdish-led Syrian Democratic Forces who are battling Daesh.
Sporadic clashes have erupted over the past two weeks as Iraqi government forces moved to retake territory that was under federal control before IS blitzed across the country in 2014. The clashes have recently moved near the border with Syria.
Army Col. Ryan Dillon said on Thursday that the fighting has "negatively impacted Coalition efforts to defeat Daesh, specifically the inability to move military equipment and supplies to our partners both in Iraq and Syria."
Iran's Supreme Leader Ayatollah Ali Khamenei said he supported efforts by the Iraqi government to ensure its "unified sovereignty and territorial integrity."
That's according to a report on the official website for Khamenei.
The website quoted Khamenei as making the comments during a visit on Thursday with Al-Abadi.
Khameni also reportedly warned Al-Abadi about US policy toward Iraq, saying: "Be careful about Americans deceit and never trust them."
Al-Abadi reportedly replied: "We protect the unity and integrity of Iraq with high precision ... we will not allow the danger of disintegration to put our country at risk."
Iraqi prime minister has announced a multi-pronged operation to capture a series of towns and villages near the Syrian border from the Islamic State group.
Al-Abadi's statement issued early on Thursday said the operation aims to liberate Al-Qaim and Rawa, as well as other villages — the very last remaining strongholds of IS militants in Iraq.
Al-Abadi, who's in an official visit to Iran, says Daesh terrorists only to choose "death or surrender."
Iraqi state TV aired live footage showing military vehicles advancing in a wide desert area, along with Shiite-dominated paramilitaries known as the Popular Mobilization Forces.
Daesh has been driven out of most of the territories it seized in 2014, from northern Iraq through the country's central region and across the western Anbar province.
The Kurdish leadership is saying that Iraqi troops have launched "an offensive" against Kurdish fighters near the border with Turkey.
From Baghdad, a spokesman for the mostly Shiite militia fighters known as the Popular Mobilization Forces says the Kurdish troops opened fire on the Baghdad-led forces as they moved toward the Iraqi Turkish border on Thursday.
The development is part of a recent government push to deploy forces in areas claimed by both the Kurds and the central government in Baghdad.
The spokesman, Ahmed al-Asadi, told The Associated Press that the clashes did not result in any casualties.
The statement from the Kurdish regional government says the Iraqi forces were "using heavy artillery... advancing toward peshmerga positions."
Sporadic clashes have erupted over the past two weeks as Iraqi government forces moved to retake territory that was under federal control before the Islamic State group blitzed across the country in 2014.
The moves follow a controversial referendum last month in which the majority of Kurds voted for independence from Baghdad.
Iraq's prime minister said he would only accept a full cancellation of the Kurdish independence vote and its results, dismissing a proposal by the autonomous Iraqi Kurdish region to freeze the referendum results pending negotiations with Baghdad.
Al-Abadi said the central government "will accept only the cancelling of the referendum and following the constitution," according to a written statement released by his office.
Al-Abadi's announcement comes during a visit to Iran on Thursday.
The Kurds' referendum last month overwhelmingly backed independence from Baghdad. Though the vote was non-binding, it has roiled tensions with the central government and the region.
Sporadic clashes have erupted over the past week between Kurdish and Iraqi forces, former allies in the battle against the Islamic State group.
Iraqi Kurdish leaders on Wednesday offered to freeze the referendum results in order to facilitate talks with Baghdad and end the violence.
Al-Abadi was in Iran after recent stops in Turkey and Jordan, and meetings with US officials and allies eager to pull Baghdad into their political orbit.
He first attended an official reception at a government estate north of Tehran and is meeting with Senior Vice President Eshaq Jahangiri on Thursday.
Regional issues and bilateral ties are expected to dominate the agenda, as well as the Iraqi Kurds' independence referendum last month that both Baghdad and Tehran have dismissed as illegal.
Iran remains a major player in the war against the Islamic State group and culturally across Iraq, its one-time bitter enemy when Iraqi dictator Saddam Hussein waged an eight year war on Iran in 1980s that left more than one million casualties on both sides.