However the US-led coalition operating in the area said it had seen no evidence of military changes in Manbij.
A UK-based monitoring group said Syrian troops and loyal militia had deployed in the area around the city.
US-backed Kurds withdrew and invited Syrian forces to replace them amid fears that Turkish troops would attack.
Turkey considers the US-backed Kurdish YPG forces to be part of a terrorist group.
The Kurds' request to the Syrian government followed the shock announcement that all US troops are to withdraw from Syria.
But that claim has been disputed by important allies who say the move could lead to a resurgence of IS.
What have the key players said?
The Syrian army said it had raised a flag in Manbij. In a televised statement, a spokesman said the troops were there to "crush terrorism and defeat all invaders and occupiers".
However Nura al-Hamed, deputy head of the Manbij local authority, told AFP that the Syrian army deployment would "not enter the city of Manbij itself but will deploy on the demarcation line" with Turkish-backed Syrian rebels
US and French coalition forces in the area remained at their positions and were continuing to conduct patrols, Ms Hamed told AFP.
The US-led coalition against the Islamic State group said reports of changes to military forces were "incorrect".
Russia, which has been fighting on the side of Syrian President Bashar al-Assad since 2015, said the arrival of Syrian government troops would "help stabilise the situation".
"The enlargement of the zone under the control of government forces... is without doubt a positive trend," said Kremlin spokesman Dmitry Peskov.
Effort to deter Turkey
By Martin Patience, Middle East Correspondent, BBC News
The consequences of President Trump's surprise announcement to withdraw all US troops from Syria are now being seen on the ground.
Manbij is a strategically important town in northern Syria that until today was under the control of US-backed Kurdish forces.
The Kurds - who led the fight against IS - see Mr Trump's decision as a betrayal.
What's the context?
Turkey has been intensifying its military activity near positions held by Kurdish fighters since President Trump's withdrawal announcement on 19 December.
US soldiers have been working closely with Kurdish forces who form part of an alliance - the Syrian Democratic Forces (SDF) - in the battle against IS.
But this policy has infuriated Turkey, which is battling the militia in the nearby city of Afrin.