The protests were the first since the ruling military council and civilian opposition agreed in principle to a power-sharing arrangement ahead of elections. The deal has yet to be finalized and signed.
A meeting between the two sides planned for Saturday was postponed to Sunday, a leader of the Forces for Freedom and Change (FFC) coalition told Reuters.
African Union mediator Mohamed Hassan Lebatt said on Thursday the council and FFC would meet on Saturday to study and ratify a constitutional declaration. They had agreed to a political declaration that determines the transition's different institutions, he said.
Several hundred also demonstrated in Khartoum's Burri neighborhood, a working-class district and the cradle of many of the protests. Troops from the paramilitary Rapid Support Forces stood on roads surrounding Burri, armed with sticks.
Security forces used barbed wire to block a main road leading to the Defence Ministry compound, the site of the protest camp crushed by security forces on June 3, a Reuters witness said.
At least 128 people were killed during the raid and in the two weeks that followed, according to doctors linked to the opposition. The government confirmed at least 61 deaths.
Across the Blue Nile, hundreds protested in the neighborhoods of Shambat and al-Mazad in Khartoum North.
In Khartoum's twin city of Omdurman, hundreds demonstrated on al-Arbaeen Street, a major artery.
Thousands also turned out in Wad Madani, the capital of Jazeera state. Hundreds more protested in Port Sudan, capital of Red Sea state, and Al-Ubayyid, capital of North Kordofan.
"There are infiltrators and intelligence services within the Rapid Support (Forces)," said General Mohamed Hamdan Dagalo, the deputy head of the Transitional Military Council.
"Rapid Support are not angels, but we prosecute every offender ... were it not for Rapid Support, Khartoum's situation would have been different."Dagalo, known by his nickname Hemedti, also heads the Rapid Support Forces, whose members are accused of violently dispersing the sit-in outside the Defence Ministry.