An aircraft or missile flew over a Sudanese military factory shortly before it exploded and burst into flames on Wednesday, residents said, but a top official dismissed their comments.
An AFP reporter several kilometres away saw two or three fires flaring across a wide area, with heavy smoke and intermittent flashes of white light bursting above the state-owned Yarmouk facility in southern Khartoum.
"I heard a sound like a plane in the sky, but I didn't see any light from a plane. Then I heard two explosions, and fire erupted in the compound," said an area resident who asked to be identified only as Faize.
Witnesses said the explosions started at about midnight on Tuesday.
A woman living south of the Yarmouk compound also reported two initial blasts.
"I saw a plane coming from east to west and I heard explosions and there was a short length of time between the first one and the second one," she said, asking not to be named.
"Then I saw fire and our neighbour's house was hit by shrapnel, causing minor damage. The windows of my own house rattled after the second explosion."
Abdul Rahman Al-Khider, the governor of Khartoum state, told official media that preliminary investigation found that the explosion happened in a store room.
He dismissed speculation that "other reasons" caused the incident.
Khider said some people were hospitalised because of smoke inhalation but he gave no numbers.
AFP could not reach the army's spokesman, Sawarmi Khaled Saad, but he was quoted by the state's SUNA news agency as saying the fire occurred at an ammunition facility in the Yarmouk complex.
The blaze spread to a neighbouring area of grass and trees, he said, adding that an investigation was underway to find the cause.
In 1998 Human Rights Watch said that a coalition of Sudanese opposition groups had alleged that Sudan stored chemical weapons for Iraq at the Yarmouk facility but government officials strenuously denied the charges.
In August of that year United States cruise missiles struck the al-Shifa pharmaceutical factory in North Khartoum, which the US said was linked to chemical weapons production. Evidence for that claim later proved questionable.
The sprawling Yarmouk facility is surrounded by barbed wire and set back about two kilometres (miles) from the district's main road, meaning signs of damage were not visible later Wednesday when an AFP reporter visited.
But at least three houses in the neighbourhood had been punctured by shrapnel which left walls and a fence with holes about 20-centimetres (eight inches) in diameter, the reporter said.
There was also slight damage to a Coca-Cola warehouse.
A source familiar with the Yarmouk factory said its main compound and storage area had not been damaged by the explosions or fire.
Hannan, a resident who gave only one name, said some people had fled the area on foot because of the early-morning explosions, while others put their children in cars ready to make a getaway.
The fires appeared to be extinguished by 03:30 am (0030 GMT), more than three hours after they began, an AFP reporter said.
There have been other mysterious blasts in Sudan.
On the country's Red Sea coast in May one person was killed when a car exploded, about a year after Sudan blamed Israel for an air strike on a vehicle in the same area. Witnesses to the May incident said they heard a big blast that set the car ablaze and left two holes in the ground.
In January 2009, foreign aircraft struck a truck convoy reportedly laden with weapons in eastern Sudan.
A September report from the Small Arms Survey, a Swiss-based independent research project, said evidence from weapons packaging suggests that Chinese-origin arms and ammunition are exported to the Yarmouk facility.
From there they have subsequently moved to Sudan's far-west Darfur region which has been plagued by conflict for almost a decade, the report said.
Small Arms Survey said it was not clear whether Yarmouk served simply as a recipient "or whether they repackage or even assemble the Chinese-made weapons."
Khartoum is seeking the removal of United States sanctions imposed in 1997 over support for international terrorism, its human rights record and other concerns.