At war with the regular army since April 2023, the RSF seized El-Fasher on Sunday, pushing the army out its last stronghold in the western Darfur region after a grinding 18-month siege.
Since the city's fall, reports have emerged of summary executions, sexual violence, attacks on aid workers, looting and abductions, while communications remain largely cut off.
A report by Yale University's Humanitarian Research Lab on Friday said fresh images gave them reason to believe much of the population may be "dead, captured, or in hiding".
The lab identified at least 31 clusters of objects consistent with human bodies between Monday and Friday, across neighbourhoods, university grounds and military sites.
"Indicators that mass killing is continuing are clearly visible," the lab said.
Survivors from El-Fasher who reached the nearby town of Tawila have told AFP of mass killings, children shot before their parents, and civilians beaten and robbed as they fled.
Hayat, a mother of five who fled El-Fasher, said that "young men travelling with us were stopped" along the way by paramilitaries and "we don't know what happened to them".
The UN said more than 65,000 people have fled El-Fasher but tens of thousands remain trapped.
Around 260,000 people were in the city before the RSF's final assault.
The RSF claimed to have arrested several fighters accused of abuses on Thursday, but UN humanitarian chief Tom Fletcher questioned the RSF's commitment to investigate violations.
Both the RSF and the army have faced war crimes accusations over the course of the conflict.
El-Fasher's capture gives the RSF full control over all five state capitals in Darfur, effectively splitting Sudan along an east-west axis, with the army controlling the north, east and centre.
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