Sudan’s military has confirmed its retreat from the besieged city of El Fasher in Darfur, as human rights groups warned that the paramilitary fighters now in control there are shooting civilians trying to flee.

The fall of the city after an 18-month siege amplified fears that the paramilitary fighters — who also control most of western Sudan’s Darfur region — could embark on a spree of ethnically motivated killings.

El Fasher had become one of the worst battlegrounds of the brutal civil war between Sudan’s military and the paramilitary Rapid Support Forces that is now stretching into its third year. Its fall to the paramilitaries means that Sudan’s military has now ceded its last major outpost in Darfur, a sprawling region the size of France.

The Rapid Support Forces, or R.S.F., redoubled efforts to capture El Fasher in April after they were expelled from the Sudanese capital, Khartoum. After months of escalating attacks with drones and heavy artillery, the R.S.F. captured El Fasher’s main military base on Friday, scattering Sudanese troops and allied Darfuri fighters into residential neighborhoods.

Sudanese military officials initially insisted that their forces were fighting on, but by late Monday they had abandoned the city. In a televised address, Sudan’s military chief, Gen. Abdel Fattah al-Burhan, said the retreat was intended “to spare citizens and the rest of the city from destruction.”

By then, accusations were already circulating on social media and from aid groups that R.S.F. fighters were chasing and sometimes killing civilians as they fled the city.

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