At least 13 Sudanese protesters have reportedly died after security forces began trying to break up a long-running demonstration in the capital Khartoum.

Protesters at a sit-in have been engaged in a weeks-long standoff with the military commanders who toppled dictator Omar al-Bashir in April.

Although the downfall of the autocrat was led by an alliance between the army and civilian demonstrators, the two sides have since fallen out over the creation of a transitional government.

The main protest organisers have accused the army of carrying out a “massacre” but the generals have denied the claims.

The military has insisted it will hand over power to a civilian administration in due course, but the protesters have refused to leave the streets until they are allowed to lead the handover.

Although the transitional military council had pledged not to use force to disperse the sit-in outside its headquarters, Sudanese troops began moving in on the demonstrators early on Monday morning.

Gunfire heard as military moves in on protesters in Khartoum Show all 10 1 /10 Gunfire heard as military moves in on protesters in Khartoum Gunfire heard as military moves in on protesters in Khartoum Sudanese forces are deployed around to disperse protesters taking part in a sit-in outside the army headquarters in Khartoum AFP Gunfire heard as military moves in on protesters in Khartoum Tyres are set alight as soldiers move in to disperse protesters outside of the military headquarters in Khartoum AFP/Getty Gunfire heard as military moves in on protesters in Khartoum A protester reacts as soldiers move in to disperse protesters outside of the military headquarters in Khartoum AFP/Getty Gunfire heard as military moves in on protesters in Khartoum Protesters build a wall to block soldiers as they move in to disperse protesters AFP/Getty Gunfire heard as military moves in on protesters in Khartoum Tyres are set alight as soldiers move in to disperse protesters outside of the military headquarters in Khartoum AFP/Getty Gunfire heard as military moves in on protesters in Khartoum Sudanese soldiers escort civilians away from the scene of a protest in Khartoum AP Gunfire heard as military moves in on protesters in Khartoum Sudanese forces are deployed around to disperse protesters taking part in a sit-in outside the army headquarters in Khartoum AFP/Getty Gunfire heard as military moves in on protesters in Khartoum Protesters build a wall to block soldiers as they move in to disperse protesters AFP/Getty Gunfire heard as military moves in on protesters in Khartoum Police officers run down a street in Khartoum as sudanese forces are deployed around to disperse protesters taking part in a sit-in outside the army headquarters in Khartoum AP Gunfire heard as military moves in on protesters in Khartoum Protesters flee as soldiers move in to disperse a sit-in being staged outside the military headquarters in Khartoum Reuters

Witnesses in Khartoum have reported gunfire, black smoke and the sight of protesters running in terror. Roads leading to the sit-in have also been blocked by soldiers.

Arab TV stations have shown chaotic footage of people running away as security forces apparently torch their tents.

The group spearheading the protests said: “The protesters holding a sit-in in front of the army general command are facing a massacre in a treacherous attempt to disperse the protest.”

It also called on ordinary Sudanese to take to the streets and stop the military crushing its sit-in.

The demand has been heard in Khartoum’s twin city of Omdurman – which sits just across the Nile from the capital. Thousands there have blocked roads with stones and set tyres on fire, Reuters has reported.

Four die in Sudan protests as military rulers say they won't allow 'chaos'

A local doctors’ association linked with the protesters said at least 13 people had died during the clashes with security forces.

But the military leaders have insisted they are not trying to violently break up the demonstrators.

The military council’s spokesperson, Lieutenant General Shams El Din Kabbashi, denied that authorities were trying to clear the protest camp and said the raid was only targeting criminals.

“The protest camp has not been dispersed,” Mr Kabbashi said. “The security forces were trying to disperse unruly elements in the Colombia area, near the protest site, and some of these elements fled to the protest site and caused this chaos.”

The council was still committed to a political settlement and was ready to resume talks, Mr Kabbashi added, speaking before the alliance called off the negotiations.

The British ambassador in Khartoum, Irfan Siddiq, tweeted he could hear “heavy gunfire” from his home.

“Extremely concerned by the heavy gunfire I’ve been hearing over the last hour from my residence and reports that Sudanese security forces are attacking the protest sit-in site resulting in casualties.