The Transitional Military Council (TMC) had “decided to disperse the sit-in”, Spokesman Shams al-Din Kabashi said on Thursday, Al-Jazeera reported.
Protesters had staged the weeks-long sit-in outside the army headquarters in Khartoum overthrowing long-time leader Omar al-Bashir in April.
But the pro-democracy protesters have continued their agitation demanding the TMC, which took over from al-Bashir, hand power to a civilian-led transitional body.
In early June, days after talks between protest leaders and the military collapsed, armed men in military fatigues broke up the camp in an operation that doctors said left 120 people dead. Doctors said that at least 40 bodies were recovered from the Nile River. The health ministry has put the nationwide death toll for that day at 61.
“We ordered the commanders to come up with a plan to disperse this sit-in. They made a plan and implemented it … but we regret that some mistakes happened,” Kabashi added on Thursday.
At the end of the conference, Kabashi stated that the plan was to clear a nearby area called Colombia, usually inhabited by drug peddlers, but then “we regret what happened”.
He noted that the findings of an investigation into the incident would be released on Saturday.
Kabashi also claimed “more than one coup attempt had been planned” against the TMC but were prevented in recent days, with “two groups of officers” taken into custody.
Kabashi’s comments came after protesters, who had staged a nationwide civil disobedience movement to demand civilian rule, agreed on Tuesday to end the campaign and resume talks with the generals.
Traffic jams have returned to downtown Khartoum and some shops in the capital’s famous gold market began to reopen on Thursday as more residents and office employees ventured out.
Fewer troops and members of the feared paramilitary Rapid Support Forces, accused by protesters and rights groups of leading the crackdown, were on the streets in downtown Khartoum, according to an AFP correspondent who toured parts of the capital.
But they were deployed in force in the northern district of Bahari, a bastion of protests against the TMC and al-Bashir, who was on Thursday charged with corruption.
“Today is my first day to work after the campaign ended but I’m not in the mood to work,” Suheir Hassan, an employee at a government office, told AFP news agency, adding, “On my way, I passed by the sit-in area and remembered that all those voices who used to chant revolutionary slogans have now disappeared.”
Following Ethiopian mediation efforts, Washington’s newly appointed special envoy to Sudan, Donald Booth, and the assistant secretary of state for Africa, Tibor Nagy, met TMC chief General Abdel Fattah al-Burhan on Thursday.
Al-Burhan told the envoys that Sudan and its people had a positive view of US efforts to reach a political settlement, according to a statement released by the TMC.
Washington said Booth had been named to help craft a “peaceful solution” to the crisis that has rocked the northeast African country.
The Alliance for Freedom and Change umbrella protest movement said its leaders had briefed the two US officials on Wednesday on the need for a transparent investigation into the June killings.
They also called for the withdrawal of “militias” from the streets in Khartoum and other towns, the lifting of an internet blockade and the establishment of a civilian administration, it said in a statement.
The African Union, which suspended Sudan following the crackdown, announced global efforts were being made to resolve the crisis.
The US diplomats were also expected to meet top envoys from Saudi Arabia, the United Arab Emirates and Egypt in Khartoum. Experts say the three key regional powers back the generals.
Days after al-Bashir’s overthrow on April 11, Saudi Arabia and the UAE offered a $3bln aid package to Khartoum, including a $500m cash injection into the central bank to help support the Sudanese pound, which has plunged against the dollar.
The country’s worsening economic crisis was one of the initial triggers for protests against al-Bashir’s three-decade rule.
On Thursday, prosecutors charged him with corruption and “possessing foreign funds, acquiring suspect and illegal wealth” and putting in place a state of emergency, state media reported.
Last month, Sudan’s public prosecutor ordered the questioning of al-Bashir, who is being held in Khartoum’s Kobar prison, over money-laundering and “financing terrorism”.
Talks between the protest leaders and generals collapsed in mid-May over the question of who should lead a new governing body – a civilian or a soldier.
Relations worsened following the crackdown, with protest leaders now insisting any agreement reached with the military rulers must be backed by “regional and international” guarantees.
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