Sudanese protesters said Tuesday that security agents loyal to ousted President Omar al-Bashir attacked their sit-ins overnight, setting off clashes that killed four people, including an army officer, and heightened tensions as the opposition holds talks with the military.

The protesters and the transitional military council said the violence was instigated by al-Bashir loyalists from within the security forces. Over his 30-year rule, al-Bashir formed several paramilitary groups outside the regular army and police.

The killings took place after nightfall on Monday, when protests in Sudan usually swell during the Muslim holy month of Ramadan that is marked by dawn to dusk fasting.

The military removed al-Bashir from power on April 11 after four months of mass protests, in which security forces have killed around 100 protesters and at least five soldiers who tried to protect the demonstrators.

On Monday, Sudanese prosecutors announced that they have charged al-Bashir with involvement in killing and incitement to kill protesters during the uprising, according to the state news agency SUNA. It was not immediately clear what punishment he might face.

Sudanese people gathered late Monday as protests continued near the site of the military headquarters in central Khartoum. (Ashraf Shazly/AFP/Getty Images)

Al-Bashir is also wanted by the International Criminal Court on charges of war crimes and genocide linked to the Darfur conflict in the 2000s. But Sudan's ruling military council has said it would not extradite him to the ICC at The Hague.

The Sudan Doctors Committee, which is part of the Sudanese Professionals Association that has been spearheading the protests since December, reported the four fatalities after initially saying there were six. The clashes took place in several locations across the country, including the ongoing sit-in area outside the military headquarters in the capital, Khartoum, the union said.

Ahmed Rabie, a spokesperson for the SPA, said more than 200 people were wounded. The military council confirmed the death of an army major and said three troops were wounded.

Amnesty International said Tuesday that uniformed security officers were captured Monday on a widely circulated social media video whipping protesters, while doctors affiliated with the Sudan Doctors Committee said they treated 40 injuries arising from whipping and breathing problems from tear gas.

The SPA said remnants of al-Bashir's regime are stoking violence, hoping it will lead to the breakup of the sit-ins. The group urged protesters to remain peaceful.

"The military council is responsible for restoring security, protecting citizens and cracking down on the remnants of the ousted regime, its security apparatus and shadow brigades," it said.

Military denies firing at protesters

In Khartoum, the clashes erupted as the protesters were expanding their sit-in area and setting up barricades made of burning tires and tree branches to block off major streets.

The U.S. Embassy also blamed the military council, saying its attempts earlier in the day to remove roadblocks, and its use of tear gas against protesters, led to the violence later that night.

The SPA said the road closures were in response to the military council's delay in handing over power to civilians. It has called for another march on Tuesday, and protest leaders have threatened a general strike and civil disobedience.

Taka Ossman Isaac, a negotiator for the Forces for the Declaration of Freedom and Change, which represents the protesters, said late Monday the negotiations were "fruitful."

A protester flashes the victory sign while holding her child in a street leading to the sit-in outside the Sudanese military headquarters on Tuesday. (The Associated Press)

Rabie said negotiations would resume later Tuesday on the makeup of a transitional sovereign council, cabinet and legislative body, and on the duration of the transition.

The protesters have called for a four-year transition overseen by a civilian-led government, while the military council has said it would rule the country for up to two years until elections can be held.

Gen. Abdel-Fattah Burhan, head of the military council, condemned the overnight violence, accusing unnamed "circles" of trying to "abort a deal" between the council and the opposition.

Gen. Hashim Ahmed, the military chief, told reporters it "did not fire a single bullet on the Sudanese people" during the overnight violence.