Members of the Sudanese security forces have shot and killed six people, including an army officer, in overnight clashes with protesters behind the uprising that drove Omar al-Bashir from power last month, a medical union said.

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

The focus of the violence appears to have been close to the central Nile Avenue in the capital, Khartoum. Most of those injured and killed were protesters manning several barricades that have sprung up around the sit-in that has occupied a large central area for more than a month.

Hours earlier, Sudanese prosecutors announced they had charged Bashir with involvement in killing and incitement to kill protesters during the uprising, according to the state news agency SUNA.

Bashir is also wanted by the international criminal court (ICC) on charges of war crimes and genocide linked to the Darfur conflict in the 2000s, but Sudan’s ruling military council has said it will not extradite him to the ICC at The Hague.

The shootings were the first serious violence since the first few nights of the sit-in – beginning on 6 April – when more than 20 people including soldiers were shot and killed by the feared National Intelligence and Security Services.

The latest violence broke out shortly after both sides in talks to create an interim joint military-civilian ruling council had announced that they had almost concluded a deal.

The shooting continued for several hours and broke out after protesters had begun to break their Ramadan fast with the traditional Iftar meal. One protester, seen by the Guardian, had been shot in his leg on Nile Avenue while manning one of the barricaded checkpoints where those entering the occupied area are searched.

Said Mohamed Ali, who was also manning a barricade when the shooting broke out, said it had been impossible to identify those responsible. “We don’t know who was shooting because it was too dark,” he said.

Both the protesters and the ruling military council said the violence was instigated by Bashir loyalists from within the security forces. Over the course of his 30-year rule, the deposed president formed a shadowy security apparatus made up of several paramilitary groups.

The US embassy, however, blamed the military council, saying its attempts earlier in the day to remove roadblocks, and its use of teargas against protesters, led to the violence later that night.

Local media suggested some of the assailants appeared to be wearing military uniform, including that of Sudan’s Rapid Support Forces (RSF), the paramilitary force behind counterinsurgency campaigns in Darfur and other regions that is led by Gen Mohamed Hamdan Dagalo, the deputy head of the military council, who is widely known by his nickname Hemedti.

A few hours before the shooting, a heavily armed RSF convoy was seen on the streets nearby.

The attackers were strongly condemned, however, by the head of the transitional military council, Abdel Fattah al-Burhan, who said they were “trying to abort agreement with the forces of freedom and change”, as the opposition coalition is known.

Burhan pointed to the peaceful character of the Sudanese revolution, adding: “The army is committed to protecting the protesters and we will arrest the perpetrators and we will hold them accountable.”

Shamael Elnoor, a political analyst, blamed the transitional military council for the violence. “What happened last night is the responsibility of the military council. The people who shot the protesters I believe are from the RSF. Most of them are young recruits.”

Many in the protest movement are concerned that remnants of the Bashir regime may try to sabotage any transition to a more democratic Sudan.

The violence prompted scenes of chaos, with ambulances ferrying the wounded from the site of the sit-in to hospitals across the capital, while protesters called for blood donations.

As protest leaders encouraged people to remain at the sit-in, and searches at the entrance were redoubled, crowds chanted: “Prepare your coffin. It is you or your country.”