The death toll from the revolt now stands at 76, with about 60 officers still missing.
Lieutenant General MA Mubin, the army second-in-command, vowed that the rank-and-file guards who turned on their superiors would be punished.
"The BDR troops who took part in these barbaric and grisly acts cannot be pardoned and will not be pardoned," he said in a national television address on Saturday.
"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."
Sheikh Hasina, who took office as Bangladesh's prime minister two months ago, had promised a general amnesty for those who surrendered but after meeting with relatives of the dead officers she promised that the amnesty would not apply to those responsible for the killings.
"No one has the right to kill anyone," she said.
General Moeen U Ahmed, the army chief, met Hasina at her home in Dhaka on Friday, apparently to discuss the situation and underline the army's support for the government.
"Let me tell you all again that the Bangladesh army is subservient to the government," Ahmed told reporters.
Tensions in the BDR erupted into violence on Wednesday when senior officers rejected appeals for more pay, subsidised food and holidays.
The guards agreed to put down their arms only after Hasina appeared on national television and threatened to put down the mutiny by force.
Following the border guards' surrender on Thursday, search teams moved into the Bangladesh Rifles compound that houses the guards and many of their families.
Firefighters used crowbars to pry off manhole covers and recover more corpses stuffed into sewers.
"The scene is horrific," Nicolas Haque, reporting for Al Jazeera from Dhaka, said.
"As you approach the area where the mass grave has been found there is the terrible smell of death, flies everywhere. Army officers, digging up the bodies, are in tears to see their own officers dead and mutilated."
About 300 BDR troops are being held by the authorities following the mutiny, but Haque reported that thousands more had fled the scene of the killings.
"As you walk through the compound you can see disregarded uniforms left, right and centre ... we presume that many [of the BDR troops] have fled the scene in some haste. You can see their guns are still there, their clothes are still there," he 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."
Sheikh Mizanur Rahman, who is heading the rescue operation, said no stone would be left unturned in the hunt for the missing senior military personnel.
"We are uncovering every manhole, looking at every piece of land," he said.
A mass funeral for the 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 erupted from the guards' longtime frustrations that their pay has failed to keep pace with soldiers in the army, anger aggravated by the rise in food prices that has accompanied the global economic crisis.
The guards earn about $100 a month.