In the capital’s twin city of Omdurman, security forces fired tear gas at demonstrators opposed to last month’s coup.
They had rallied to pay tribute to dozens of colleagues killed by Sudanese security forces in recent weeks.
They also denounced a recent deal with the military that saw Prime Minister Abdalla Hamdok reinstated to his post.
Prominent political parties and Sudan’s powerful protest movement have opposed Mr Hamdok’s decision to sign the accord with the military.
Some have called it a betrayal or said it provided political cover for the coup.