“There was heavy firing of tear gas after which army soldiers opened the gates of the compound for protesters to enter,” a witness told AFP.
“A few minutes later a group of soldiers fired gunshots in the air to push back the security forces who were firing tear gas.”
A second witness too said soldiers had intervened against the security force agents.
An AFP correspondent, some five kilometres (three miles) away from the headquarters, heard shooting for about four minutes.
Since the protests erupted in December, the armed forces have remained on the sidelines even as security agents and riot police have cracked down.
Demonstrators have called on the army to protect them from the deadly crackdown, after days of camping outside its headquarters, which also houses Bashir’s residence and the defence ministry.
‘Wish of the revolution’
Defence Minister General Awad Ibnouf vowed that the army would prevent any slide into chaos.
“Sudan’s armed forces understand the reasons for the demonstrations and is not against the demands and aspirations of the citizens, but it will not allow the country to fall into chaos,” Ibnouf said on Monday, according to the official SUNA news agency.
In a separate statement, army chief of staff Kamal Abdelmarouf said the military was “discharging its responsibility in securing and protecting citizens.”
Officials say 38 people have died in protest-related violence since December.
Interior Minister Bushara Juma said seven protesters died and 15 were wounded on Saturday when forces tried to disperse them.
He said 42 security personnel were injured and 2,496 arrests made.
The umbrella group spearheading the protests appealed to the army on Monday for talks on forming a transitional government.