"The U.S.is withdrawing from northeast Syria in a strong, deliberate and coordinated manner, and seeks to ensure that the forces that have fought alongside coalition partners in the campaign against ISIS are not mistreated", an administration official said following the president's tweet.
Turkey's planned military operation against a Kurdish militia in Syria does not depend on an American withdrawal from the region, Ankara said on Thursday.
A Defense Department spokesperson later said that while equipment was being moved out of Syria, troops were not withdrawing.
President Donald Trump last month claimed that ISIS had been defeated in Syria and said all USA troops were "coming back now".
That provoked Turkish President Recep Tayyip Erdogan to snub Trump's national security adviser last week, after John Bolton had received a warm welcome by Israeli officials days before.
The comments from Hulusi Akar, on an unannounced visit to inspect troops stationed near the Syrian border directly opposite territory held by the US -backed Kurdish YPG, appeared to be aimed at both Washington and its Kurdish allies.
The surprise announcement came in a statement from Col. Sean Ryan, the spokesman for the United States-led coalition against the Islamic State.
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Air strikes and special forces have played key roles in efforts to claw back the territory lost to ISIS.
US Secretary of State Mike Pompeo, who has been touring the Middle East this week to reassure allies of Washington's commitment to regional security, said on Saturday he was "optimistic" a way could be found to protect Syrian Kurds while allowing Turks to defend their country despite a US pullout from Syria.
A Kurdish-led group, the Syrian Democratic Forces, is now flushing the jihadists from the last pockets of land they control in the Euphrates River Valley.
Trump's decision to withdraw all of the 2,000 U.S. troops from the war-torn country prompted shockwaves among USA senior officials and United States allies in December.
The battle against die-hard militants in remote areas along the Iraqi-Syrian border and the hunt for ISIS supremo Abu Bakr al-Baghdadi, the world's most wanted man, could last indefinitely. The withdrawal benefits Syrian President Bashar Assad and his worldwide backers, Russian Federation and Iran, who are primed to move into the region to fill a vacuum left behind by the Americans.
Since Trump's announcement, senior members of his administration including Bolton and Secretary of State Michael Pompeo have frustrated Turkey by setting more specific conditions on what Trump initially suggested would be a quick withdrawal.