Sudan accused Israel of attacking a military factory in the capital killing two people, 18 months after alleging a similar raid by the Jewish state.
Culture and Information Minister Ahmed Bilal Osman said four radar-evading aircraft carried out an attack at around midnight Tuesday (2100 GMT) on the Yarmouk military manufacturing facility in the south of the city.
Evidence apparently pointing to Israel's involvement was found among remnants of the explosives, he told a news conference on Wednesday.
Residents living near the Yarmouk factory told AFP an aircraft or missile had flown over the facility shortly before the plant exploded in flames.
An AFP reporter several kilometres away saw two or three fires flaring across a wide area, with thick smoke and intermittent flashes of white light bursting above the state-owned factory.
"We think Israel did the bombing," Osman said. "We reserve the right to react at a place and time we choose."
The military and foreign ministry in Israel, which has long accused Khartoum of serving as a base for militants from the Palestinian Islamist group Hamas, refused to comment.
Sudan took its case to the UN Security Council Wednesday with envoy Daffa-Alla Elhag Ali Osman calling on the council to condemn Israel.
"We reject such aggression and expect your esteemed council to condemn this attack because it is a blatant violation of the concept of peace and security" and the UN charter, the ambassador said.
The envoy also accused Israel of arming rebels and helping to transport rebel leaders in Sudan's Darfur region, where the UN says at least 300,000 people have been killed over the past decade.
Israel was "jeopardising peace and security in the entire region," he said.
Sudan's cabinet held an urgent meeting on Wednesday but issued no statement afterwards. Outside the cabinet office about 300 protesters denounced the United States and carried banners calling for Israel to be wiped off the earth.
"The army of Mohammed is returning," they shouted.
In 1998, Human Rights Watch said a coalition of opposition groups had alleged that Sudan stored chemical weapons for Iraq at the Yarmouk facility. Government officials strenuously denied the charge at the time.
In August of that year, US cruise missiles struck the Al-Shifa pharmaceutical factory in North Khartoum, which Washington alleged 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 (one mile) from the main road, so signs of damage were not visible later Wednesday when an AFP reporter visited.
But at least three houses in the neighbourhood had been hit by shrapnel, which left walls and a fence with holes about 20-centimetres (eight inches) in diameter
In Khartoum the minister, Ahmed Bilal Osman, said Yarmouk made "traditional weapons".
"The attack destroyed part of the compound infrastructure, killed two people inside and injured another who is in serious condition," he said.
There have been other mysterious blasts in Sudan -- and allegations of Israeli involvement.
In April last year, Sudan said it had irrefutable evidence that Israeli attack helicopters carried out a missile and machine-gun strike on a car south of Port Sudan.
Israel refused to comment but officials there had expressed concern about arms smuggling through Sudan.
Last year's attack mirrored a similar strike by foreign aircraft on a truck convoy reportedly laden with weapons in eastern Sudan in January 2009.
Khartoum is seeking the removal of US sanctions imposed in 1997 over its alleged support for international terrorism, its human rights record and other concerns.