An army officer who managed to escape the guards holding him told the news agency AFP how the guards opened fire indiscriminately.
"It was cold-blooded murder," Syed M Kamruzzaman said.
"They hurled abuse at us and gunned down whoever they wanted. I was shot at seven times and was lucky to get out alive."
Officials said more than 230 guards had been arrested in Dhaka and 68 more near the town of Savar.
Checkpoints were set up across the country and ferries were being searched for fleeing mutineers.
The guards, demanding better pay and conditions, surrendered on Thursday after Sheikh Hasina Wajed, the prime minister, threatened to put down the mutiny by force and sent tanks into the streets of Dhaka.
A day earlier, Hasina offered the mutineers an amnesty and agreed to look into their demands.
But on Friday, Hasina said the amnesty would not apply to those who carried out the killings.
"No one has the right to kill anyone," she said.
It remained unclear whether the amnesty would apply to the guards who tried to flee.
Al Jazeera's Nicolas Haque, reporting from Dhaka, said relatives of missing officers were gathering outside the BDR compound in a restless crowd.
"Despite Sheikh Hasina's promises that she would forgive the mutineers and that the army would not intervene, mutineers have been arrested inside the compound and the army is taking control of the area," he said.
"Some of the mutineers have tried to flee the compound, dressed in civil clothes, but the police managed to catch them overnight."
Manzoor Hasan, the director of BRAC University's Institute of Governance Studies in Dhaka, said the attack had taken the country and prime minister Hasina by surprise.
|Relatives of missing officers gathered outside the compound [Reuters]
"It was a bit of a baptism by fire for her. It was a critical test, but I think in the end she tackled it competently," he said.
The violence is the first major crisis facing the prime minister since she was elected in late December, when Bangladesh returned to democracy after nearly two years of army-backed emergency rule.
Hasan said it would be a mistake to follow through with a promise of general amnesty.
"It's up to the prime minister and the government to restore discipline to the BDR quickly and take stern action on those responsible. Encouraging impunity is not a good look."
The mutiny began at the BDR compound in Dhaka, where nearly 2,000 guards opened fire on their senior officers and seized their headquarters.
Police chiefs across the country said BDR members had revolted in 15 border districts.
The BDR is led by army officers and it has been a contentious issue with the troops, who want commanders to be drawn from their own ranks.
The main duty of the BDR is to guard the country's borders, but they often back up the army and police.