In Khartoum on Saturday, thousands protested on Sitteen Street, a major thoroughfare in the capital, a Reuters witness said.
Footage and photos posted by the SPA showed thousands of people demonstrating in the capital and its sister city of Omdurman.
Protesters rallied in the eastern cities of Madani and Kassala and in the central city of Al-Obeid, witnesses told AFP by telephone.
Sudan has been in political deadlock since the overthrow of autocratic President Omar al-Bashir in April.
Demonstrators in Khartoum chanted slogans against the country's military leadership and held signs reading "Justice for the martyrs".
The agreement stipulates that the new governing body will be presided over by a military nominee for the first 21 months, and by a civilian for the last 18 months.
The protests in December swiftly escalated into nationwide demonstrations against the autocrat's ironfisted three-decade rule.
The protests finally led to the army ousting him on April 11, but the generals who seized power have so far resisted demonstrators' demands to hand it over to a civilian administration.
The military council insists it did not order the raid, which according to the protest movement killed more than 100 and wounded hundreds in just one day. The transition agreement sets up a joint Sovereign Council that will rule for a little over three years while elections are organized.
Ibrahim said that the armed forces, rapid support forces, security, intelligence, and police will remain keen on the security and stability of the country and secure the gains and achieve the highest national goals and access to power through the ballot box, according to the Sudanese News Agency.
Intensive mediation of the African Union and Ethiopia led to a July 5 consensus on forming a "civilian and military" sovereign council to manage the country.
"This is an attempt to block the agreement which has been reached by the Transitional Military Council and the Alliance for Freedom and Change", Sudanese Gen. Jamal Omar said on state television.
The raid came after talks between the generals and protest leaders collapsed in May over who should lead the new governing body - a civilian or soldier.