But participants say the new military rulers are a continuation of al-Bashir's former regime and have clamoured for more concessions.
Al-Bashir, whose 30-year rule came to an abrupt end last week, has been under the custody of the army.
Crowds have dwindled during the day due to the scorching heat, but protesters still gather in the thousands after breaking the fast in the evening for the Muslim holy month of Ramadhan.
The Sudanese Professionals Association said in a statement seen by Anadolu Agency that the events have escalated in the square of the sit-in in front of the General Command of the Sudanese Armed Forces.
One policeman and three protesters were killed in Khartoum and many other demonstrators were wounded, state TV said.
However, the TMC has said that the military would never fire on peaceful protestors.
The sit-in has become the focal point for the protest movement in place of the near daily protests that had been held around the country while the veteran president remained in power. "What happened last night is the responsibility of the military council".
A Sudanese protester gestures as they burn tyres and barricade the road leading to al-Mek Nimir Bridge crossing over Blue Nile; that links Khartoum North and Khartoum. It was not immediately clear what punishment he might face.More news: Lenovo release more information, sizzle video for folding Lenovo Thinkpad X1 laptop
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The charges form part of an investigation into the death of a medic killed during a protest in the capital's eastern district of Burri, his office said in a statement.
The issue has kept protesters camped outside army headquarters around the clock ever since Bashir's overthrow. It has called for another march on Tuesday, and protest leaders have threatened a general strike and civil disobedience.
The protesters are represented by the Forces for the Declaration of Freedom and Change, a coalition of opposition groups.
Both said they had agreed on the duties and authorities of sovereign, executive and legislative bodies.
The Transitional Military Council plans to remain in power for two years, but protesters and many in the worldwide community want it replaced with a civilian government.
Other footage showed men from the Rapid Support Forces forcibly dispersing protesters.
"We discussed the structure of the transitional authority and agreed on it completely, and we also agreed on the system of governance in the transitional period", said Lieutenant General Shams al-Din Kabashi, spokesman of the transitional military council.
The dispersal came as stalled talks between the opposition and the ruling Transitional Military Council (TMC) resumed.