"Civilians from the market converged on the Unamid (the joint peacekeeping force) camp and they are still coming," Kemal Saiki, the Unamid communications chief, said.
Suleiman Sandal, the Jem commander, denied that the group had been pushed out of Muhagiriya, saying it had withdrawn voluntarily to spare the population from government air attacks.
"We felt that the government would continue to bomb the civilians while we were there. So we withdrew a long distance from the town," he told the Reuters news agency.
Hundreds of civilians, including women and children, fled the fighting in the town over the past three weeks and arrived at displacement camps in north Darfur, a Unamid statement said.
There has been speculation that the increase in violence in Darfur is tied to a decision expected by the International Criminal Court (ICC) on whether to issue an arrest warrant for Omar al-Bashir, Sudan's president, for suspected war crimes.
Ban Ki-moon, the UN chief, warned in a report issued Wednesday that an arrest warrant by the ICC could have an adverse impact on UN personnel in Sudan.
"I am concerned about remarks by some of its officials that the [Sudanese] government may redefine its relationship with Unmis [UN mission in Sudan] should an arrest warrant be issued against President al-Bashir," he said.
International experts say 200,000 have died and 2.7 million have fled their homes since Darfur rebels started a war against Sudan's government in 2003.
Khartoum disputes these figures, claiming that only 10,000 have died.