Gunfire was heard from military bases operated by the Sudanese intelligence Service in Khartoum as some members of the facility mutinied against various reforms, the military said.
The camps in Kafouri, north of Khartoum and Riyadh which hosts the Operations Corps, involved a group of soldiers who were protesting against a move to send home some, have their units disbanded and merged with another.
The gunfire renewed fear among residents of Khartoum who had lived the last six months in relative tranquility, but were now in the vicinity of another violent incident.
It all began as members of the National Security Intelligence Service refused to leave the premises of the Operations Corps as ordered.
A statement by the Sudanese intelligence stated that a soldiers opposed to the restructuring of the agency, and demanding pay and severance packages engaged a violent protest, causing a stand-off.
The statement released on Tuesday after the incident said the matter will be investigated.
Reacting on the development, Sudanese Prime Minister said the situation was under control.
"We assure our citizens that the events that occurred today are under control and they will not stop our march or cause a retreat from the goals of the revolution. The current situation proves the need to confirm the current partnership and push it forward to achieve higher goals. We renew our confidence in the armed and regular forces and their ability to control the situation," tweeted Hamdok.
Sudan is undergoing various security reforms that could see some units of the military disbanded, merged or have their operations limited.
The Operations Corps, for example, was a unit that guarded key military installations and often gathered intelligence in times of conflict. It is to be disbanded. Some of the soldiers relieved of duties and the remaining ones appended to what used to be the Rapid Support Forces, recently enjoined in the army.
The RSF itself was a paramilitary unit that emerged from the feared Janjaweed militia known for their deadly maiming during the Darfur war. The International Criminal Court had accused some of their members of killing and raping as well as running a scorched-earth policy in Darfur region.
The military official explained that "all options are open to controlling these uncertainties.
In the camp of the intelligence agency in Khartoum, gunfire erupted, causing residents fear, and it was decided to close the roads leading to the operations authority in the Riyadh and Kafouri neighbourhoods.
Earlier in the day, members of the General Intelligence Service refused to hand over the buildings of the operations authority, despite instructions to vacate them.
A statement issued by the Sudanese General Intelligence Service stated that a group of employees of the Operations Authority objected to the procedures of structuring the agency, the value of the financial reward, and after-service benefits.
The statement, published Tuesday, said that the situation is being evaluated after a number of employees of the Operations Authority objected to the structural procedures, in accordance with the country's national security requirements.
Sudanese army spokesperson, Brigadier General Amer Muhammad Al-Hassan, said that a group of intelligence services in the country had carried out what he considered a "rebellion" in protest against their weak financial entitlements, stressing that the "chaos" requires urgent and decisive action.
He added that the military “condemns behaviour carried of some of forces of the intelligence agency today [Tuesday], after demanding better pay” and that the security apparatus in Khartoum will move to “resolve the chaos.”