With the assault, the generals signaled an end of their tolerance of the pro-democracy demonstrators, who for months have been camped outside the military's headquarters as the two sides negotiated over who would run the country after the April ouster of longtime strongman Omar al-Bashir.
The head of the military council said early Tuesday that protest leaders shared blame for the violence, accusing them of dragging out negotiations and seeking to keep other sectors of Sudanese society out of an interim government. Gen. Abedel-Fattah Burhan also said that the council was cancelling all its agreement with protest groups and would call elections within seven months.
After their protests succeeded in forcing the military to remove al-Bashir, pro-democracy demonstrators had stayed in the streets, demanding the generals move to the background and allow civilians to lead the transition.
The dispersal of the sit-in now risks escalating violence even further. Scattered by the bloody assault, protesters vowed to keep up their campaign, suspending talks and calling for a general strike and civil disobedience. They urged nighttime marches across the country.
"This is a critical point in our revolution. The military council has chosen escalation and confrontation," said Mohammed Yousef al-Mustafa, a spokesman for the Sudanese Professionals' Association, which has spearheaded the protests.
"Those are criminals who should have been treated like al-Bashir," he said. "Now the situation is either them or us, there is no other way." Burhan's statement said military leaders would investigate Monday's violence. He didn't mention security forces, but said protests leaders bore blame for the volatile situation, because they have been "extending the negotiations and seeking to exclude other political and security forces" from participating in any transitional government.
The council and protest leaders had made progress during talks in May over an interim Cabinet and legislative body, but they split over the make-up and leadership of a sovereign council that was being discussed to govern Sudan during a three-year transition.
Burhan said the military council would now move to form an interim government to prepare for elections, which he said would be internationally supervised. He said the council was cancelling all its agreements with protest leaders.
Earlier, the military council said in a statement that Monday's violence erupted when security forces tried to clear an area adjacent to the protest camp. It said people being chased by the troops fled into the sit-in site, leading to the shooting deaths and injuries.
Activists said the assault appeared to be a coordinated move, with other forces attacking similar sit-ins in Khartoum's sister city of Omdurman and the eastern city of al-Qadarif. The attack came on the day before the Eid holiday that ends Ramadan, the holy month when Muslims fast during daylight hours. Large numbers of troops from the military, police and Rapid Support Forces — an elite unit that during the anti-al-Bashir protests had vowed to protect the sit-in — moved in on the gathering after overnight rains, activists said.
"They are surrounding the sit-in from all directions," one activist, Amal al-Zein, said early in the assault, in which the forces burned tents and arrested those trying to flee. An Associated Press journalist heard gunshots and explosions, and saw buses and soldiers on foot blocking roads leading to the protest site. In online videos, protesters were seen running and ducking as barrages of gunfire echoed. Smoke rose from tires set ablaze by the protesters.
Demonstrators stood behind low barricades of bricks and dug-up pavement, and some threw stones before being driven back by walls of blue-clad security forces carrying sticks. One video showed police swarming around a protester sprawled on the ground, beating him with sticks. In another video, residents opened their doors to shelter those who ran.
The Sudan Doctors' Committee said the death toll had risen to at least 35 by early Tuesday with the killing of five people in the city's Bahri district. The group said it was difficult to count deaths in areas outside the military complex in Khartoum. Hundreds of people were wounded, many by gunfire, the group said.
Medical personnel and wounded were trapped in clinics as troops overran the area. "Wounded people are lying on the ground in the reception area as there are not enough beds," said Dr. Azza al-Kamel of the Royal Care hospital.
Hundreds were arrested, said al-Zein and another activist, Hisham Shalabi. Photos posted online showed dozens of men and women lined up on the pavement, sitting or lying face down, under guard by troops.
The assault ended the sit-in at the heart of the movement that echoed the 2011 Arab Spring uprisings — although Sudan's sought to learn from the mistakes of other protesters. Protest leaders insisted the removal of al-Bashir after 30 years in power was not enough. Tens of thousands remained in place in Khartoum and other camps around the country, demanding a fast transition to civilian rule.
The negotiations had imposed a degree of peace. But tensions mounted in recent weeks as the talks yielded little progress. Protesters demanded the military have only limited involvement in a transitional government, but the generals have resisted relinquishing power.
Just over a week ago, Burhan met with his two top allies, the president of Egypt and the crown prince of the United Arab Emirates. Those leaders backed al-Bashir's removal and have given strong support to the military council. They also deeply oppose movements such as those that swept the region in 2011.
After Monday's violence, the Sudanese Professionals' Association called for closing main roads to "paralyze public life" across the country. The Forces for Declaration of Freedom and Change, which has represented protesters in the negotiations, called for toppling the military council and more street protests.
U.N. Secretary-General Antonio Guterres condemned the crackdown and called for authorities to allow an independent investigation, his spokesman Stephane Dujarric said. "There was use of excessive force by the security force on civilians," Dujarric said.
The U.N. human rights chief, Michelle Bachelet, expressed alarm at reports that live ammunition was used, including "next to, and even inside, medical facilities." The embassies of the United States and Britain also expressed concern. Amnesty International urged the U.N. Security Council to consider imposing sanctions on members of Sudan's ruling military council.
The military "has completely destroyed the trust of the Sudanese people and crushed the people's hope for a new era of respect for human rights and respect for the right to protest without fear," said Sarah Jackson, Amnesty International's deputy regional director for East Africa.
Associated Press writer Bassam Hatoum reported this story in Khartoum and AP writer Samy Magdy reported from Cairo.