The recently reinstated prime minister sacked the director-general of the police and his deputy after medics accused security forces of targeting protesters with live ammunition.
Prime Minister Abdallah Hamdok has replaced Sudan's police chiefs after more than 40 people were killed in a crackdown on protests following last month's military coup.
Hamdok said he had sacked on Saturday the director-general of the police, Khaled Mahdi Ibrahim al Emam, and his deputy, Ali Ibrahim.
In their place, he appointed Anan Hamed Mohamed Omar with Abdelrahman Nasreddine Abdallah as his deputy, the premier said in a statement.
Medics say at least 42 people were killed as security forces sought to crush weeks of anti-coup demonstrations, with protests continuing even after Hamdok's release from house arrest and return to his post last week.
They have accused security forces of targeting protesters in the "head, neck and torso" with live ammunition, as well as with rubber-coated bullets and tear gas canisters.
The police have denied reports they opened fire using live bullets.
Moreover, while several civilian leaders have been released since last Sunday's deal, key figures are also still in detention.
Hundreds of political activists, journalists, protesters and bystanders watching the rallies have been arrested in recent weeks, and remain in custody.
On Friday, three Sudanese political figures arrested since the coup started a hunger strike in protest at their continued detention.
Military chief General Abdel Fattah al Burhan seized power and detained Hamdok on October 25, but after international condemnation and mass protests he reinstated the premier in a November 21 deal.
The deal raised hopes for some that Sudan will be able to return to its tenuous transition process.
But critics slammed the agreement as "whitewashing" the coup, with some protesters accusing Hamdok of "treason" by signing it.
Hamdok, who has headed a transitional government since the 2019 ouster of long-time autocratic ruler Omar al Bashir, said Wednesday he partnered with the military in order to "stop the bloodshed" and "not squander the gains of the last two years".
The deal he signed with Burhan lays down a "clear date" for Sudan's first free elections in three decades slated for July 2023, the premier said.