Sudan's public prosecutor has set up a committee to investigate violence at the main protest site outside the Defense Ministry headquarters in Khartoum, state news agency SUNA said on Monday.

A doctors committee close to the protest movement in Sudan reported that 13 people had been killed and more than 100 injured during violence as security forces evacuated a sit-in camp outside the Ministry of Defence in the Sudanese capital Khartoum on Monday morning.

The representatives of the protest movement, the Alliance of Freedom and Change (AFC), and the TMC had been negotiating over the issue of civilian-military representation in power during the interim phase following the army's ouster of president Omar Al-Bashir amid mass protests against his 30-year-old rule.

The Transitional Military Council (TMC) had offered to let protesters form a government but insisted on maintaining overall authority during an interim period. Demonstrators want civilians to run the transitional period and lead Sudan's 40 million people to democracy.

Talks were suspended on Monday..

Thousands of young men and women have been taking turns to camp outside the Ministry of Defence, a focal point of anti-government protests that started in December.

The doctors committee reported a "large number of critical casualties and urged the Sudanese people to aid the injured, also called for "urgent support" from the International Committee of the Red Cross and other humanitarian organisations.

The military council’s spokesman, Lieutenant General Shams El Din Kabbashi, said the raid targeted criminals and that the protesters were safe.

“The protest camp has not been dispersed,” 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 on a civilian transition soon, Kabbashi added.

After news of the evacuation spread, protesters poured into the streets in Khartoum and its twin city of Omdurman, on the opposite side of the River Nile.

Television footage showed black smoke rising from tents, apparently torched by the raiding during evacuation. Demonstrators blocked roads with rocks and burning tyres, witnesses said.

Demonstrators, some waving Sudanese flags, hurled stones at security forces, who charged amid sounds of intense gunfire.

A Reuters witness saw troops wielding batons deployed in central Khartoum and close roads.

Bridges over the Nile have also been blocked.

There were no signs of any security forces in Omdurman.

Meanwhile, The Umma Party, the country's oldest opposition party, called for nationwide protests.

The United States, Britain, African Union, United Nations and the European Union expressed deep concern about the situation and called for restraint and the end of violence.