"The BDR troops who took part in these barbaric and grisly acts cannot be pardoned and will not be pardoned," lieutenant general MA Mubin said in a national television address.
"They will be given exemplary and quick punishment by a special tribunal. The martyrs will be buried with state honours."
Jahangir Kabir Nanak, a cabinet minister, said: "These senior military personnel have been killed in a planned and calculated manner. It's a grisly slaughter. We will punish these criminals."
Firefighters had a day earlier uncovered the bodies of dozens of senior officers, killed during the force's two-day mutiny and hurriedly dumped into shallow graves and sewers.
Tensions in the BDR erupted into violence on Wednesday after senior officers rejected appeals for more pay, subsidised food and holidays.
The guards agreed to put down their arms, and later fled after Hasina appeared on national television and threatened to put down the mutiny by force.
Firefighters and emergency workers moved into the BDR compound housing the guards and their families and discovered corpses stuffed into sewers.
"The scene is horrific," Nicolas Haque, reporting for Al Jazeera from Dhaka, said.
"Where the mass grave has been found there is the terrible smell of death and flies are everywhere.
"Army officers, digging up the bodies, are in tears to see their own officers dead and mutilated."
About 300 BDR troops have been arrested and thousands remain at large after fleeing the compound following the killings.
"As you walk through the compound you can see discarded uniforms left, right and centre ... You can see the [guards'] guns are still there, their clothes are still there," Haque said.
"There were more than 9,000 BDR troops that were here and the vast majority of them are nowhere to be found. There's a manhunt organised by the army to try and find these people."
A mass funeral for the dead military personnel was expected to be held once all bodies had been recovered.
Bangladesh has been observing three days of national mourning since Friday.
The insurrection is believed to have erupted over frustrations among the guards, who earn about $100 a month, that their pay has failed to keep pace with soldiers in the army.
Their anger was futher aggravated by the rise in food prices that has accompanied the global economic crisis.