"Our forces are in their best condition," Abdel Fattah al-Burhan told army commanders at the headquarters close to the city centre and airport.
The army's recapture of the General Command of the Armed Forces is its biggest victory in the capital since reclaiming Omdurman, Khartoum's twin city on the Nile's west bank, nearly a year ago.
In a statement on Friday, the army said it had merged troops stationed in Khartoum North (Bahri) and Omdurman with forces at the headquarters, breaking the siege of both the Signal Corps in Khartoum North and the General Command, just south across the Nile River.
Since the early days of the war, when the paramilitary Rapid Support Forces (RSF) quickly spread through Khartoum, the military had to supply its troops inside the headquarters via airdrops.
Burhan was himself trapped inside for four months before emerging in August 2023 and fleeing to the coastal city of Port Sudan.
The recapture of the headquarters follows other gains for the army.
Earlier this month, troops regained control of Wad Madani, just south of Khartoum, securing a key crossroads between the capital and surrounding states.
- 'Disregard for human life' -
With the army gaining ground in central Sudan, the RSF has set its sights on consolidating its hold on Darfur, where it controls every state capital except El-Fasher.
Despite besieging it since May, the paramilitary has not managed to wrest control of the city from the army and its allied militias.
Days after it issued an ultimatum demanding army forces and their allies leave the North Darfur state capital, an attack on the city's Saudi Hospital on Friday killed 70 people and injured dozens, the United Nations said on Sunday.
"The attack, reportedly carried out by the Rapid Support Forces (RSF) on the only functional hospital in El-Fasher, is a shocking violation of international humanitarian law," the UN's resident and humanitarian coordinator in Sudan, Clementine Nkweta-Salami, said Sunday.
"The alarming disregard for human life is unacceptable," said the UN's most senior official in Sudan.
The RSF on Sunday accused the army and its allies of striking the hospital.
The late Friday drone strike destroyed the hospital's emergency building, a medical source told AFP.
World Health Organization chief Tedros Adhanom Ghebreyesus said on X the "appalling" attack took place while "the hospital was packed with patients receiving care".
Both sides have been accused of targeting civilians and indiscriminately shelling residential areas, with the RSF specifically accused of ethnic cleansing, systematic sexual violence and laying siege to entire towns.
The United States announced sanctions this month against RSF leader Mohamed Hamdan Daglo, accusing his group of committing genocide.
A week later, it also imposed sanctions against Burhan, accusing the army of attacking schools, markets and hospitals, as well as using food deprivation as a weapon of war.
- 'The best medicine is peace' -
The war in Sudan has unleashed a humanitarian disaster of epic proportions.
Tens of thousands of people have been killed and, according to the United Nations, more than 12 million uprooted.
Famine has been declared in parts of Sudan but the risk is spreading for millions more people, a UN-backed assessment said last month.
Particularly in the country's western Darfur region and in Kordofan in the south, families have been forced to eat grass, animal fodder and peanut shells to survive.
"Above all, Sudan's people need peace. The best medicine is peace," Ghebreyesus said.
During Sunday prayers in Rome, Pope Francis lamented how the country has become the site of "the most serious humanitarian crisis in the world".
He called on both sides to end the fighting and urged the international community to "help the belligerents find paths to peace soon".
bur-maf/bha/ami
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