Officials said that the army has been called in to bring the situation under control.
Nicholas Haque, reporting for Al Jazeera from Dhaka, said there had been heavy fighting since the morning.
"The fighting broke out, apparently, this morning during a meeting between junior and senior officers. There is panic on the streets right now. No-one is clear about what's happening," he said.
"They [a suspected paramilitary group] are shooting into civilian crowds around them.... it's a very terrible reminder of what happened years ago when there was a coup.
'Mutiny over pay'
"Fighting continues in the compound. There is no security, no police, there is no-one outside the compound... there are just civilians... apart from the army pointing their guns towards civilians."
Private TV stations Bangla Vision and ETV, reporting live from the scene, said the guards came out of their barracks and seized a conference hall where officers were meeting.
The report said troops of the Bangladesh Rifles chanted slogans for more pay and better facilities.
Several bystanders outside the complex were injured and taken to state-run Dhaka Medical College Hospital, ETV reported.
Some of the troops also stormed out of the complex and seized a nearby shopping mall, ETV added.
The fighting occurred a day after Sheikh Hasina, the newly elected prime minister, visited the headquarters and addressed the troops, urging them to become "more disciplined and remain ever ready to guard the country's frontiers".
Bangladesh has had a history of military coups and uprisings.Mujibur Rahman, Bangladesh's first elected president and the father of Hasina, was killed along with several of his family members in 1975.
The country, which secured its independence from Pakistan in 1971, has also experienced long spells of military rule.