Soldiers set up road blocks across the country after many mutineers fled under cover of darkness. Troops from the Bangladesh Rifles (BDR), a paramilitary unit that patrols the country's borders, rose up against their commanders earlier this week.
Commander AK Azad, a spokesman for the elite Rapid Action Battalion, said more than 230 mutineers, who had discarded their uniforms, were rounded up on Thursday night in the capital, Dhaka. Dozens more were picked up 25 miles outside the city.
Security forces have set up highway checkpoints to search buses and are also boarding ferries as they look for more mutineers.
What is emerging is a sorry tale of bloody insubordination on a vast scale. More than 2,000 guards opened fire on their senior officers and seized their headquarters in Dhaka on Wednesday in a rebellion over poor pay.
The rebels wore red bandanas and sprayed bullets into the unit's officer corps at an annual "durbar", a meeting where the rank and file can bring their grievances to the officer corps.
There had been simmering resentment by the paramilitaries, who earn $100 a month, over the practice of appointing army officers to head the BDR. The border guards also do not participate in UN peacekeeping missions, which attracts additional pay.
Eyewitnesses told television channels that the mutineers led 11 officers out and shot them in cold blood. The commanding officer, Major General Shakil Ahmed, was reportedly mown down in a hail of gunfire, although authorities refuse to confirm any details.
"I was confronted by the soldiers three times, but I have survived," one of the officers, Lieutenant Colonel Syed Kamruzzaman, told ATN Bangla television station. "Allah has saved me from the face of death."
The official death toll of the bloody two-day revolt stands at 22 – many of them senior BDR officers – but it is reported that 34 bodies were recovered from a hole 15ft deep inside the BDR's military complex today and more than100 senior officers are still missing.
The crisis was the first real test for the new prime minister, Sheikh Hasina, who kept her nerve when it appeared the mutineers would not back down. She sent in tanks and warned the rebels they were on the path to suicide.
There were also real fears of a military putsch, a political reality in a country which as seen almost 20 failed coup attempts since it gained independence from Pakistan in 1971.
After two years under an army-backed "caretaker" government, the return to democratic rule in Bangladesh last month was never likely to be smooth.
The recriminations are likely to have a traumatic effect on Bangladesh's morale.
"The prime minister has said there will be clemency," said Shahedul Anam Khan, a retired brigadier general. "I can understand the amnesty for troops who defied the chain of command. But for those that took part in cold-blooded murder there will be no mercy. An army and a country cannot function otherwise."