Thousands had rallied in front of the compound in Khartoum since the weekend, in one of the biggest demonstrations since protests erupted in December calling for President Omar al-Bashir to step down.
The protesters set up tents on Saturday, in what appeared to be an effort to replicate the mass sit-ins of the Arab Spring uprisings of 2011. On Monday, security forces used tear gas, rubber bullets and live fire to try to disperse the protesters, according to the Sudanese Professionals Association, which is spearheading the demonstrations.
The Sudan Doctors Committee, an affiliate of the SPA, said a soldier was fatally wounded while trying to protect the protesters. It said at least 90 people were wounded in the attempt to disperse the sit-in. Later in the day, the committee said security forces killed a 20-year-old man in Khartoum's twin city of Omdurman.
Footage posted online by activists showed soldiers moving peacefully among the protesters, raising the possibility that some troops were trying to halt the violence without force. Another clip showed a truck carrying a group of soldiers, including one who was wounded.
The union leading the protests called on the military to back the "people's choice" to end al-Bashir's rule and said they are seeking "direct communications" with its leadership to "facilitate a peaceful transfer of power to a transitional government."
During the 2011 uprising in neighboring Egypt, the army stepped in to prevent clashes between protesters and police, and ultimately forced President Hosni Mubarak from power. It was unclear whether such a scenario was underway in Sudan, where media access to the demonstrations has been heavily restricted. There was no immediate comment from the military.
The county's interior minister, Bishara Gomaa, told the parliament on Monday that at least seven people were killed in the protests since Saturday — six in Khartoum and the seventh in the Darfur region. He said 2,496 people were arrested in Khartoum.
Protesters said security forces in pickups, mostly from the feared National Intelligence and Security Service, attacked the sit-in early Monday, firing tear gas, rubber bullets and live ammunition. Activist Amal el-Zein said soldiers guarding the compound stood by at first, but then moved in to chase the security forces away, firing into the air.
Another activist said security forces later repeated their attempt to break up the sit-in, forcing protesters to seek shelter in a nearby navy facility. He said the military has deployed troops around its headquarters and blocked several roads leading to the complex. The activist spoke on condition of anonymity, fearing retaliation.
The protests were initially sparked by price hikes and shortages, but quickly escalated into calls for the resignation of al-Bashir, who seized power in 1989 in an Islamist-backed military coup. Al-Bashir has refused to step down and has also declared a state of emergency. Dozens of people have been killed in the crackdown so far.
The protests gained momentum last week after Algeria's President Abdelaziz Bouteflika, in power for 20 years, resigned in response to weeks of similar protests. Also Monday, U.N. spokesman Stephane Dujarric urged authorities to release all detained protesters. He said the United Nations is following the demonstrations closely and is ready to support any efforts agreed on by the Sudanese to peacefully resolve the crisis.