US troops leaving Syria for Iraq hit a hurdle Tuesday after Iraq said it hadn't given permission for them to regroup there.

US defense secretary Mark Esper said Monday troops would be re-stationed along the Iraq-Syria border, with a mission to secure oil fields and monitor ISIS activity.

But the Iraqi government poured cold water on Esper's plan, saying the US had not secured the necessary permission to puts its troops on their territory.

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The US military found its plans for its chaotic withdrawal from Syria further mangled on Tuesday, when the government of Iraq said it had not given permission for troops to resettle on its soil.

Defense Secretary Mark Esper had told reporters Monday that the US troops evacuating Syria would be redeployed along the Iraq-Syria border, with a mission to secure oil fields and operate in a limited capacity against ISIS.

But less than a day after that announcement, the Iraqi government said that the US had not secured the necessary permission to puts its troops on their territory.

In a statement issued to reporters Tuesday afternoon, the Iraqi government said that troops coming from Syria have permission to transit through US bases and airfields, but not to settle there.

A US military convoy stops near the town of Tel Tamr, north Syria, October 20, 2019. AP

"All US forces that withdrew from Syria received approval to enter the Kurdistan Region so that they may be transported outside Iraq. There is no permission granted for these forces to stay inside Iraq," the statement said, according to a translation by Reuters.

The statement explicitly contradicts what was announced the previous day by Esper and President Donald Trump, throwing and not to, throwing the plan into chaos.

Read more: Video appears to show US troops being pelted with stones and rotten fruit as they pull out of Syria

The dispute is the latest in a string of missteps by the Trump administration over its military presence in northeastern Syria, which began when the president gave a green light to a Turkish military operation aimed at clearing Kurdish forces off the shared Syria-Turkey border.

Boys wave towards a convoy of U.S. vehicles withdrawing from northern Syria, in Erbil. Reuters

Over the course of the last two weeks, US troops were ordered to abandon their Kurdish partners in the five year fight against ISIS.

After a hasty retreat from their bases, US forces saw them occupied by Russian fighters, amid a bipartisan outcry in Washington, D.C., at the spectacle of Trump abandoning longtime US allies.

The confusion over basing rights comes as the Iraqi government finds itself mired in a political crisis that has seen over 100 people killed while protesting government corruption and the influence of Iranian-backed militias in the country.

US. Vice President Mike Pence visited Turkey to discuss a ceasefire in late October. Reuters

A Kurdish official working in Erbil, part of the semi-autonomous Kurdish region in northern Iraq, described the chaos to Insider.

Read more: The life of Turkish President Recep Tayyip Erdogan, who survived a coup, bent an entire nation to his will, and owned Trump over Syria

Speaking under anonymity to describe events in the Iraqi central government, he said: "The government in Baghdad is under massive attack by its own people tired of corruption and foreign influences and this [bases] situation will put them under more pressure from Iran, which wanted these troops out of Syria but not so they could remain in Iraq."

"We are close with the Americans and are happy to invite these troops as guests in the, but we are not sure exactly what the US is requesting or how Baghdad will respond to any request," the official said.

By Tuesday afternoon it was unclear if any US troops exiting Syria for Iraq had departed the region or if talks would be opened with the Iraqis to determine the fate of the proposed deployment.

The US has also agreed — in talks with Israel and Jordan — to maintain a base of about 150 special forces troops in the Syrian town of Tanf, which straddles the main highway linking Syrian regime territory and Iraq.

This deployment is mostly designed to deny Iran free ground passage between Iraq and Syria.