Later on Wednesday, Sudan asked the United Nations Security Council to condemn Israel for violating the country’s sovereignty and bombing the factory.
In response to a question about the attack, Israeli Minister for Military Affairs Ehud Barak said, "There is nothing I can say about this subject."
In May, Khartoum said Israel launched a missile attack on a car in Port Sudan, which killed one person.
Sudan also accused Tel Aviv of carrying out a similar attack on a car near Port Sudan in April 2011.
The Israeli regime, however, has neither denied nor confirmed involvement in the incidents.
A US-based non-profit monitoring group has said that the explosion and fire at a military factory in Sudan this week was caused by airstrikes, which Khartoum said were conducted by Israel.
On Wednesday, Sudanese Culture and Information Minister Ahmed Bilal Osman announced that four Israeli warplanes had attacked a weapons factory in the Sudanese capital Khartoum late on Tuesday night, killing two people.
On Saturday, the Satellite Sentinel Project (SSP) said satellite photos showed six huge craters, each roughly 16 meters (52 feet) across, at the Yarmouk military factory in Khartoum.
"If the explosions resulted from a rocket or missile attack against material stored in the shipping containers, then it was an effective surgical strike that totally destroyed any container that may have remained," the SSP said, but did not point the finger at any culprit.
"The explosions destroyed two buildings and heavily damaged at least 21 others, all within 700 meters of the epicenter," added the group, which conducts monitoring of the border between Sudan and South Sudan.
"Visible damage includes roof panels blown off and scattered around the area, windows blown out, and walls knocked down," the SSP stated.