US Defence Secretary Mark Esper has denied US troops are pulling out of Iraq, after a letter from a US general there suggested a withdrawal.
The letter said the US would be "repositioning forces in the coming days and weeks" after Iraqi MPs had called for them to leave, reports BBC.
Mr Esper said there had been "no decision whatsoever to leave".
The confusion came amid threats to American forces after the US killed top Iranian commander Qasem Soleimani.
He died in a US drone strike in Baghdad on Friday on the orders of Mr Trump.
The killing has sharply increased regional tensions, with Iran threatening "severe revenge".
What was in the letter?
It appeared to have been sent by Brig Gen William H Seely, head of the US military's task force in Iraq, to Abdul Amir, the deputy director of Combined Joint Operations.
It starts: "Sir, in due deference to the sovereignty of the Republic of Iraq, and as requested by the Iraqi Parliament, and the Prime Minister, CJTF-OIR (Combined Joint Task Force - Operation Inherent Resolve) will be repositioning forces over the course of the coming days and weeks to prepare for onward movement."
The letter says certain measures, including increased air traffic, will be conducted "during hours of darkness" to "ensure the movement out of Iraq is conducted in a safe and efficient manner".
It would also "alleviate any perception that we may be bringing more Coalition Forces into the IZ (Green Zone in Baghdad)".
How has it been explained?
Mr Esper told reporters in Washington: "There's been no decision whatsoever to leave Iraq. I don't know what that letter is... We're trying to find out where that's coming from, what that is.
"But there's been no decision made to leave Iraq. Period."
The highest-ranking US soldier, Chairman of the Joint Chiefs of Staff Mark Milley, then appeared at a briefing, saying the letter was "a mistake".
He said it was a draft which was poorly worded, had not been signed and should not have been released. It was being circulated for input, including from Iraqis.
"[The letter] was sent over to some key Iraqi military guys in order to get things co-ordinated for air movements, etc. Then it went from that guy's hands to another guy's hands and then it went to your hands. Now it's a kerfuffle."
Gen Milley reiterated that US troops were not leaving.
So what is happening?
Gen Milley said the issue was being "worked" with the Iraqis, but gave no details.
BBC defence correspondent Jonathan Beale said he had been told by a coalition source that the letter was to let the Iraqis know the US was moving troops out of the Green Zone to provide protection elsewhere and did not mean a withdrawal.
This has been backed up by other coalition sources, telling separate reporters that the move was to "thin out" the Baghdad personnel.
What are the US and other forces doing in Iraq?
There are just over 5,000 US troops in Iraq, part of the Combined Joint Task Force - Operation Inherent Resolve, which was set up in 2014 to tackle the Islamic State group after it had captured a large swathe of Syria and Iraq.
There are about a dozen primary member countries, and scores more providing non-combat support.
The main focus of the task force is to train and equip Iraqi forces.
On Sunday, Iraqi MPs passed a non-binding resolution calling for foreign troops to leave in the wake of Soleimani's assassination.
President Trump then threatened severe sanctions against Iraq if US troops left.
"We have a very extraordinarily expensive airbase that's there. It cost billions of dollars to build. We're not leaving unless they pay us back for it," he told reporters.