Sudanese Prime Minister Abdalla Hamdok says he is confident in the country's military even after a rebellion this past week at the General Intelligence Service (GIS) headquarters by soldiers associated with former leader Omar al-Bashir.
The incident led to the resignation of Sudan's intelligence chief Abu Bakr Mustafa Damblab as authorities launched an investigation into the mutiny.
Mr Hamdok is trying to unify a country that has been in conflict for most of the past five decades. The prime minister sought to assure the public of security following the attempted revolt.
Last weekend, Mr Hamdok, who heads the transitional government composed of both civilian representatives and the military, made a historic trip to Kauda town in the southern Nuba Mountains to meet rebel leader Abdulaziz al-Hilu, SPLM-North group.
The visit, seen by Western diplomats as a bold step to unify the country, was however tarnished by the mutiny this past week.
"We reiterate our faith in the Sudanese armed forces and their ability to contain situations," Mr Hamdok said. "We want to assure the Sudanese people that the incidents that took place today are under control and they will not stop us and our mission nor will they be a reason for us to retreat from the goals of this revolution."
The revolt at the GIS, what used to be called the National Intelligence and Security Service under Mr Bashir, involved some soldiers whose unit, the Operations Corps, was being disbanded as part of security reforms. According to the official account, on Tuesday soldiers of the Operations Corps refused to leave the premises, protesting low pay and lack of a severance package. and engaged the Rapid Support Forces (RSF) for hours before the mutiny was quelled.
After the mutiny, forty-five armoured vehicles from the intelligence services, along with anti-aircraft guns, were recovered.
In the fracas, a family was killed in the suburb of Soba in Khartoum after a stray shell landed on their house. A father and his two children died, according to the Central Committee of Sudan Doctors, a group of medics who helped push through the revolution.
The Sudanese army also announced that two soldiers had been killed and seven others wounded in the clashes in Khartoum.
Chief of staff Lieutenant General Muhammad Othman Al-Hussein Al-Hassan said in a statement on Wednesday, that there had been "a rebellion against the authority". A committee was set up to investigate the incident and punish the perpetrators.
Mr Damblab, however, did not wait for the findings.
"The director of intelligence has resigned. He called us on phone and we asked him to submit a written resignation, so we are now considering it," Gen Abdel Fattah al-Burhan, the head of Sudan's Transitional Sovereign Council told state television on Wednesday.
Gen Burhan added that a committee formed would continue its investigations anyway to identify the people behind the confrontation.
Mr Damblab had been appointed the head of the powerful GIS shortly after the resignation of Salah Gosh in April last year.
Mr Gosh had been associated with the torture and disappearance of Mr Bashir's opponents. As Mr Bashir's regime neared its end in April, Mr Gosh quit. The US government imposed sanctions on him and his immediate family, barring him from setting foot there.
The Sudanese Professionals Association, one of the lobbies that helped push Bashir out, said in a statement that Mr Bashir's old guards had engineered the insurgency.
"The revolt of the Operations Corps of the defunct regime's security apparatus is linked to the remnants of the al-Bashir regime and his gangs who operated during his days. "It is an attempt to drag the country into the cycle of violence and undermine the gains of the glorious revolution of the Sudanese people," the Association said.
Mr Bashir was recently jailed for two years for corruption. He also faces an International Criminal Court indictment for war crimes and crimes against humanity in Darfur.
On Thursday, Gen al-Burhan spoke of a "deep state" composed of remnants of the past who were a still actively trying to undermine authority. He claimed the incident "had well been planned before."
This past week, both sides of the transitional government vowed to work together to root out distractors. Normalcy was restored in the capital and residents demanded the relocation of military bases operated by the intelligence agency in Khartoum.