Noureddine Mezni, Unamid's spokesman, said a large number of Muhajiriya residents took refuge in the peacekeepers' base during the attack.
"I can confirm the bombing took place. We are very concerned about the situation," he said.
The attacks were also confirmed by Ahmed Tugud, JEM's chief negotiator.
Tensions have been rising in Darfur as all sides of a nearly six-year-old conflict are waiting for the International Criminal Court (ICC) to decide whether to issue an arrest warrant against Omar Hassan al-Bashir, the Sudanese president, for war crimes.
No one from Sudan's armed forces was available to comment on the accounts of the raid.
But Sudan's army acknowledged its planes bombed JEM positions outside Muhajiriya last week.
Air attacks in Darfur are forbidden under a 2006 peace deal and UN Security Council resolutions.
The JEM seized control of Muhajiriya last week from forces led by Minni Arcua Minnawi, the only Darfur rebel leader to have signed a peace deal with the government in 2006.
UN officials, speaking on condition of anonymity, warned at the time that Minnawi's forces were re-grouping for a counter-attack, possibly backed by government troops.
International experts say 200,000 people have died since JEM and other rebels took up arms against the government in 2003, accusing it of neglecting the remote western region.
Khartoum mobilised mostly Arab militias to crush the rebellion. It denies activists' accusations that genocide took place during the offensive.