ISIS suicide bombers have attacked crowds fleeing the terror group's last bastion as US-backed forces have moved in, an SDF spokesperson has said.
A witness told Reuters that the terror group had sent three women suicide bombers to the area to target the families who were leaving.
Six civilians are said to have been killed with three US-backed troops having been injured by the blast.
Throughout the week civilians have been moving out of the area with their families, walking over the rocky conditions in Baghouz. With the elderly and children often having to climb up difficult paths.
A smoke plume billows from the remains of an Islamic State group jihadists' camp near the village of Baghouz in the eastern Syrian province of Deir Ezzor, on March 15
Mortars have been being launched throughout the week by the SDF on the frontline fighting to expel ISIS
The US-backed SDF having pushed militants further out of Syria and they now remain in Baghouz
An official with the Syrian Democratic Forces, who goes by the name Ciyager, said IS militants are still holding 300 prisoners, both civilians and SDF fighters, adding that their fate is unknown.
The campaign to uproot the militants from the eastern banks of the Euphrates River began in September, pushing them down towards a last corner in the village of Baghouz, near the Iraqi border.
The operation to uproot the militants has been halted several times since February 12 as the SDF said a large number of civilians and hostages were in the territory.
Earlier this week the SDF resumed its final push in the area before reducing pressure after strong resistance from the extremists.
A fighter of the US-backed Syrian Democratic Forces (SDF) looks on at the remains of an Islamic State (IS) group jihadists' camp near the village of Baghouz
This is while hundreds of IS fights and family members surrendered.
Ciyager said there are no negotiations under way to secure the prisoners' release.
An SDF statement said hundreds of IS fighters and their families surrendered on Thursday.
Today SDF spokesman Mustafa Bali tweeted that a new group of IS fighters had surrendered.
Another SDF official said an IS suicide bomber apparently approaching to surrender blew himself up at the checkpoint where they search evacuees. The official refused to say if there were casualties.
Explosions were seen at the beginning of the week in the Syrian province of Deir Ezzor
The incident underscores how risky the operation is, and how it can be difficult for forces to tell civilians from combatants.
Some fighters have surrendered in recent weeks, but hardcore militants, including many foreigners, are still holed up in the shrinking space along the eastern bank of the Euphrates River.
SDF commanders have stopped speculating when the battle may finally be over. Already 25,000 people have left Baghouz, thousands more than were originally believed inside.
Commanders say they do not know how many more may be left, hiding in tunnels beneath the war-scarred village.
On Friday the situation was quiet as aircraft flew over the area controlled by IS.