As Sudan’s Omar al-Bashir attempts to quell a popular uprising against his rule, armed clashes between different branches of his security forces threaten “civil war”, demonstrators are warning.

Protests, which began in December, have been reignited by the successful 3 April ouster of Algeria’s Abdelaziz Bouteflika, and new instability could potentially plunge the nation of 41 million deeper into chaos.

Sudanese protesters have flooded the capital Khartoum since 6 April, braving the guns and teargas of Mr Bashir’s Rapid Support Forces militia, and loyalist security branches, including the National Intelligence and Security Services, or NISS, that serves as the the presidency’s secret police.

But witnesses to the days of protests also described members of the uniformed regular military providing shelter and protection to the demonstrators, many of whom are camped out in front of the Sudan Armed Forces headquarters. The fiercest clashes erupted on Tuesday morning, with video showing intense gunfire between the rival branches of the armed forces.  

“The security forces and the militias from the government are trying to suppress the protests,” Mohamed Al-Amin, a journalist in Khartoum, told The Independent in a phone call. “Groups of national army, especially the leadership of the maritime forces, are against them. They fought the militias and security.”

Military headquarters occupied by anti-government protesters in Sudan

Show all 15

At least five soldiers of the uniformed military have already been killed in the recent round of clashes, along with at least nine protesters, who have been holding day-and-night demonstrations and sit-ins since Saturday using slogans of the 2011 Arab Spring uprisings to demand democratic change.  

Those protests yielded disastrous results across much of the Arab world, with civil war or reinvigorated dictatorship the result in all but Tunisia. A collapse of order in Sudan, already a transit point for migrants, could prompt fresh refugee flows towards Europe.

Protests first broke out in Sudan late last year, but were re-energised following events in Algeria. Mr Bashir appears to be fiercely struggling to cling to power. The country’s security services have also launched a sweeping crackdown on critical media, shutting down several publications and arresting several major journalists.

But reports of cracks within the security forces has introduced a whole new dimension of potential instability. One video posted online showed a soldier among the demonstrators, urging fellow military men to join him.

“Some parts of the military are standing tall beside the protesters,” said Hassan Ahmed Berkia, a Sudanese journalist and analyst now in the United Arab Emirates.

“It’s mostly low-ranking people in the army. The high-ranking officers are close to the government and close to Bashir’s party.”

Police also appear to be refusing to open fire on protesters, and often relenting to their demands, even if they haven’t outright joined them. On 6 April police quit their positions and allowed protesters to reach key sites inside Khartoum including the headquarters of the armed forces, a sprawling compound that includes multiple entrances for various branches.

The next day, security forces opened fire with teargas and sound bombs, to scare off demonstrators. But the armed forces opened their gates and gave the protesters shelter, and defended them from Mr Bashir’s loyalists.  

“They allowed us to move into the ministry of defence, inside the complex,” Ali Awad Ekrem, a 24-year-old Khartoum physician trainee, told The Independent. “Then they told us to lay down, and they opened fire against the militias.”

On Monday and Tuesday, Mr Bashir’s forces again attacked the demonstrators, and again the uniformed armed forces, especially the maritime division, opened its gates to give shelter to the civilians as the loyalists opened fire on protesters.

“It’s dangerous what [Bashir’s security forces] are doing,” said Mr Ekrem, who divides his time between the protest site and a clinic where he treats some of the wounded demonstrators. “They are making a war between the Bashir’s militias and the military forces. It’s the start of a civil war.”    

Mr Al-Amin said more and more Sudanese from Khartoum neighbourhoods and even other cities are joining the protests, along with increasing numbers of junior military officers disheartened by Mr Bashir’s security priorities.

“There was already anger among the national army because Bashir has given more money and salaries to the militias” he said. “Now five soldiers have been killed from the national army. Everyone considers this a very big incident that they cannot tolerate. There’s a feeling that he’s using them and sacrificing them.”

The UK, US and Norway on Wednesday issued a statement calling for a “political transition” away from Mr Bashir, who faces international war crimes and genocide charges for his conduct in the Darfur conflict. His regime is widely seen as rife with corruption and incompetence.

“The time has come for the Sudanese authorities to respond to these popular demands in a serious and credible way,” said the statement. “Failing to do so risks creating greater instability.”

But Mr Bashir’s downfall would reverberate throughout the Arab world far more than the ouster of Mr Bouteflika and likely alarm the clique of reactionary oil-rich Arabian Peninsula hereditary monarchies which support him, and their allies – including Saudi Arabia, the United Arab Emirates and Egypt. They rallied together after the 2011 Arab Spring to maintain autocratic rule throughout the Middle East and North Africa.

While Algeria’s path and alliances differ from much of the Arab world, Mr Bashir’s Sudan serves as an investment destination for Arabian Peninsula money as well as a source of recruits for the Saudi-led offensive in Yemen. The Gulf monarchies have already pumped hundreds of millions into Sudan’s coffers since the unrest began earlier this year. Russia, a backer of Syria’s dictatorship, has also reportedly dispatched security advisers to aide Mr Bashir.

Sudan’s state news agency announced the regime would organise a series of pro-Bashir rallies on Thursday. Protesters say they fear Mr Bashir, 75, will use any tool at his disposal to stay in power.

“He’s even worse than Bashar al-Assad,” said Mr Ekrem.