The UN official, speaking on condition of anonymity because of the sensitivity of the issue, said the peacekeepers opened fire when the crowd threatened the base, killing three.
After the riot and shooting which took place on Sunday in El Geneina, a town near the border with Chad, Sudanese police deployed around the peacekeepers' base.
The AU said it could not immediately comment on the case.
An AU officer in El Geneina told The Associated Press that only two people had died, and that peacekeepers opened fire because fighters carrying rocket-propelled grenades were sighted among the crowd. The officer spoke on condition of anonymity because he was not authorised to give information to the press.
AU peacekeepers have been deployed in Darfur since mid-2004 on a mission to protect Darfur's civilians in a three-year conflict that has killed more than 200,000 people and driven 2.5 million from their homes.
"Pressure must be put not only on the Sudanese government, but on the rebels, to cease hostilities and cultivate peace."
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The war pits government troops and their Janjaweed allies against ethnic African rebels. The Janjaweed are accused of atrocities including killing and raping civilians in attacks on their villages.
The shooting is likely to worsen the widespread hostility toward the force among refugees, who often complain that the peacekeepers do not prevent Janjaweed attacks.
The 7,000-strong mission has been too understaffed and under-equipped to halt the increasing violence in Darfur.
The AU said Monday that two peacekeepers were abducted and their car stolen by gunmen in the capital of North Darfur, El Fasher, late Sunday. It did not say who was believed to be behind the kidnapping.
A UN official said that a Nigerian major was among those abducted close to the house of the AU's force commander in El Fasher.
El Fasher has been the scene of looting attacks over the past week by Janjaweed who killed 10 people in the town.
But on Monday, some 500 Janjaweed and 250 Chadian rebels hired by the Sudanese government withdrew from El Fasher after the governor of North Darfur complained, the UN official said.
Mohammed Yussuf Kebir, who was appointed by Khartoum, threatened to resign unless the Janjaweed were reined in. The Janjaweed pulled out after Sudan's police chief, defence and interior ministers held high-level meetings in El Fasher on Sunday, the UN official said.
Though the government insists it does not control the Janjaweed and does not back rebels from neighbouring Chad, the UN official said these fighters were directly controlled by Khartoum's top leadership.
In a separate incident, some 43 refugees held captive by Janjaweed fighters in the West Darfur refugee camp of Zalingei were released Monday, aid workers said.
Rebels in Sudan's western region of Darfur said a government aircraft killed eight civilians, mostly children, in a northern village on Monday.
Sudan's armed forces said the report was a fabrication designed for propaganda purposes.
Jarennabi Abdel-Karim, a spokesman for a faction of the rebel Sudan Liberation Army (SLA) which refused to sign a peace agreement with Sudan's Khartoum-based government in May, said the plane fired a rocket at a house in the village of Hashaaba.
"Eight people from the same family were killed," he told Reuters via satellite telephone. "Most of them are children."
The incident could not be independently verified.