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

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, said the latest six fatalities included an army officer. 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.

The ruling military council confirmed the death of an army major and said three troops were wounded at the sit-in.

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 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.”

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.