Sudan is a "dangerous terrorist state," a top Israeli defence official said on Thursday after the Sudanese government accused Israel of carrying out a deadly missile strike on a military factory in Khartoum.

Sudanese officials say the attack on the Yarmouk facility south of Khartoum, which took place at around midnight on Tuesday and killed two people, was carried out by four radar-evading aircraft.

Israel, which has long accused Khartoum of serving as a base of support for militants from the Islamist Hamas movement which rules Gaza, has refused all comment on the claim.

"Sudan is a dangerous terrorist state. To know exactly what happened (there), it will take some time to understand," Amos Gilad told Israel's army radio.

Asked directly whether Israel was involved in the attack, Gilad, who serves as director of policy and political-military affairs at the defence ministry, refused to reply directly.

The Israeli air force, he noted, was "one of the most prestigious in the world, a fact which had been proved many times in the past.

"Sudanese President Omar al-Bashir is regarded a war criminal. Sudan has also served as the operational base for (the late Al-Qaeda chief Osama) bin Laden," Gilad pointed out.

"The regime is supported by Iran and it serves as a route for the transfer, via Egyptian territory, of Iranian weapons to Hamas and Islamic Jihad terrorists," he told the radio.

Khartoum has said it found evidence of Israeli involvement among the remnants of the explosives at the blast site.

"We think Israel did the bombing," Culture and Information Minister Ahmed Bilal Osman said, adding: "We reserve the right to react at a place and time we choose."

It is not the first mystery blast which has prompted allegations of Israeli involvement.

In April 2011, Sudan said it had irrefutable evidence that Israeli attack helicopters carried out an air strike on a car driving along its Red Sea coast which killed two people.

Israel again refused to comment, but Israeli intelligence sources told AFP that a truck carrying weapons, which was being escorted by the car, had been hit in the strike.

In January 2009, foreign aircraft bombed a convoy of trucks in eastern Sudan, with US and Israeli press reports saying they were carrying weapons destined for Gaza during Israel's deadly 22-day assault on the territory.

Khartoum, which has close ties with Hamas, is seeking the removal of US sanctions imposed in 1997 over its alleged support for international terrorism, its human rights record and other concerns.