The Kurdish-led Syrian Democratic Forces (SDF) control that territory along the Euphrates river after defeating Islamic State there over the past year with U.S. help.
Syria’s foreign ministry sent letters to the United Nations on Monday calling for an end to the “attacks and treason of the SDF militias”.
The government blamed the SDF for repressing protesters and asserted “its right to defend citizens in all corners of the country”, state media said.
The U.S.-backed SDF, which controls much of north and east Syria, denied the allegations. It said the state would have been better off working with its forces which are chasing down Islamic State sleeper cells.
The Kurdish-led civil administration of the SDF region said some had tried to exploit problems with public services.
“The regime’s adoption of groups seeking to create strife in parts of Deir al-Zor is a hit against Syrian unity,” it said.
The SDF, which the Kurdish YPG militia spearheads, has been meeting with Arab tribal leaders from Deir al-Zor in a bid to diffuse tensions.
Kurdish-led authorities accused Damascus on Tuesday of trying to incite strife by exploiting a recent wave of protests in the mainly Arab swathes of eastern Syria they hold.
Residents in Deir al-Zor province, near the Iraqi border, have taken to the streets in recent weeks with demands including better services, political representation and access to the oil-rich region’s resources.