The U.S. -backed Syrian Democratic Forces (SDF) have been laying siege to Islamic State's last enclave east of the Euphrates, the village of Baghouz, for several weeks.
An SDF official who goes by Mervan The Brave said many IS gunmen are still inside and prepared to fight.
"However, some Daesh still remain in tunnel network under the camp", he warned, using an Arabic acronym for the terror group.
The fighting in the Al Sukhna - between the historical city of Palmyra and the eastern border city of Deir Ezzor - highlights the fact that although worldwide forces are poised for the final assault on the remaining pocket of territory held by the militant group east of the Euphrates river, the threat from ISIS endures. However, he died in a mortar attack two days later. Associated Press journalists positioned across from the ISIS-held pocket saw lines of pickup trucks, motorcycles and people walking on foot, in what appeared to be a group evacuating.
In a related development, Syrian regime forces have mounted airstrikes against ISIS militants and clashed with them in central Syria, the pro-Damascus al-Watan newspaper reported on Tuesday.
The new estimate compounds the challenge of relocating the captured Islamic State fighters to their home countries and makes it harder for the US-led coalition to wind down operations in Syria, even after the extremists no longer hold territory.
In a statement released on Monday, the US-backed Syrian Democratic Forces (SDF) said it released at least 283 Syrians suspected of having ties to IS.
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"I would characterize the number of IS fighters now in SDF custody as thousands", Navy Commander Sean Robertson, a Pentagon spokesman, said in a statement, referring to the IS.
The Kurdish-led force pushed into Baghouz on Saturday.
Around 15,000 people reached Al-Hol from Baghouz between February 22 and March 1, the UN's humanitarian coordination office OCHA said on Monday.
"Everything happens outdoors, there are no houses anymore, everybody lives outside, which is not surprising because we were being bombarded day and night", she said.
The Kurdish-led forces launched their broad offensive on remaining IS strongholds in the Euphrates Valley six months ago.
The chiefs of the U.S. and Russian militaries met in Austria on Monday to discuss the situation in Syria, where a residual USA military force will remain following the territorial defeat of the IS group.
Syria's war has killed more than 360,000 people and displaced millions since it started in 2011 with the brutal repression of anti-government protests.