Sudan has warned that it has the right to retaliate after accusing Israel of carrying out an air strike on an arms factory, causing a huge explosion that killed two people.

Ahmed Belal Osman, the Sudanese information minister, said that bombs from four aircraft struck a complex and triggered a blast that rocked the capital, Khartoum, before dawn on Wednesday.

"Four planes coming from the east bombed the Yarmouk industrial complex," Belal told a press conference. "They used sophisticated technology … We believe that Israel is behind it."

Belal recalled a 2009 attack on an arms convoy in the Red Sea province in eastern Sudan, resulting in scores of deaths, which his government also blamed on Israel.

"We are now certain that this flagrant attack was authorised by the same state of Israel," he added. "The main purpose is to frustrate our military capabilities and stop any development there, and ultimately weaken our national sovereignty.

"Sudan reserves the right to strike back at Israel."

Officials showed journalists a video in which a huge crater could be seen next to two destroyed buildings and what appeared to be a rocket lying on the ground. Belal said an analysis of rocket debris and other material on the ground had shown that Israel was behind the attack.

Sudan may take the issue to the UN security council, he added.

The Israeli Defence Forces and foreign ministry both declined to comment on the Sudanese claim. Israel has a track record of carrying out operations against hostile states, but rarely acknowledges such actions. It has no diplomatic relationship with Sudan, and believes the country to have a role in arms trafficking to militant groups in Gaza.

"It has been widely acknowledged that shipments of weapons are crossing Sudan on their way to Gaza," said an Israeli government source. The weapons were not thought to originate in Sudan but Khartoum was allowing trafficking to happen, he said.

Khartoum has blamed Israel for previous attacks over recent years. In April 2011, two people were killed when a car was struck by a missile near Port Sudan."This is not the first time things have been attributed to us," said the Israeli government source.

The powerful blast at the Yarmouk complex, which was built in 1996, sent exploding ammunition flying through the air. Local resident Abdelgadir Mohammed, 31, said a loud roar of what they believed was a plane prompted him and his brother to step outside their house at around midnight.

"At first we thought it was more than one plane," he told the Associated Press. "Then we thought it was a plane crashing because of how sharp the sound was. Then we saw a flash of light, and after it came a really loud sound. It was an explosion."

Mohammed said the explosion caused panic among the residents of the heavily populated low-income neighbourhood. Many fled to open spaces, fearing their homes were collapsing. He said ammunition was flying out of the factory into the air and falling inside homes.

"It was a double whammy, the explosion at the factory and then the ammunition flying into the neighborhood. The ground shook. Some homes were badly damaged. The walls of our home cracked, so we left our house to sleep elsewhere. When we came back this morning, our beds and furniture were covered in ashes."

Thick smoke blackened the sky over the complex, and firefighters needed more than two hours to extinguish the fire.

Sudanese army spokesman Sawarmy Khaled said two people were killed and another was seriously injured. Others suffered from smoke inhalation.

The US imposed economic, trade and financial sanctions against Sudan in 1997, citing the government's support for terrorism, including its sheltering of Osama bin Laden in Khartoum the mid-1990s.