Sudanese government officials met in urgent session after accusing Israel of a deadly missile strike on a military factory in Khartoum, 18 months after alleging a similar raid by the Jewish state.

The cabinet issued no statement after its Wednesday night meeting. Outside the government 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.

Culture and Information Minister Ahmed Bilal Osman had earlier 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.

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.

Evidence pointing to Israel's involvement was found among remnants of the explosives, Osman told a news conference on Wednesday.

"We think Israel did the bombing," he said. "We reserve the right to react at a place and time we choose."

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.

Sudan took its case to the UN Security Council, where its envoy Daffa-Alla Elhag Ali Osman called 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 states, and said Israel was "jeopardising peace and security in the entire region."

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 state-linked media said 65 houses in the area had been "affected."

The Yarmouk factory made "traditional weapons", Information Minister Osman said.

"The attack destroyed part of the compound infrastructure, killed two people inside and injured another who is in serious condition," he said.

Earlier Wednesday before officials accused Israel, the governor of Khartoum state, Abdul Rahman Al-Khider, told official media that preliminary investigation found that an explosion happened in a store room.

He dismissed speculation that "other reasons" caused the incident.

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.