The palace has been held by the paramilitary force RSF (Rapid Support Forces) since the ongoing civil war broke out in April 2023. It is the force's last stronghold in the capital Khartum.
"Today, the flag is raised, the palace is back, and the journey continues until victory is complete", writes Information Minister Khaled al-Aiser on X.
The recapture can be seen as further progress for the military, which has made steady advances in recent months, including the recapture of a key refinery north of Khartum.
However, RSF claims that the battles for the palace are not over and that they have "killed more than 89 enemies and destroyed military equipment".
There are also reports that three journalists from Sudanese state TV have been killed by RSF drones.
On Thursday, RSF claimed to have taken control of the strategically important desert town of al-Maliha. The military says that fighting has been ongoing but has not acknowledged any loss of the town.
The country can be seen as divided into two: Sudan's army controls the northern and eastern parts, while RSF has taken over large parts of western and southern Sudan.
Around twelve million inhabitants have fled their homes since the civil war broke out, with over three million having left the country.
There is a lack of credible figures on the number of fatalities, with estimates ranging from 30,000 to 150,000, according to a calculation made in November 2024 by Tom Perriello, the US envoy to Sudan.