Syed Ashraful Islam, a government minister, said the decision to set up the tribunals was made at a cabinet meeting led by Hasina late on Saturday.
Wanted for murder
Meanwhile, police said that 1,000 mutineers were wanted for murder.
The government has also decided to give 1 million taka ($14,520 ) to the families of each of the victims.
On Sunday, witnesses said that about 1,000 border guards had returned and were waiting to be let inside the BDR headquarters.
Over the last two days, firefighters and emergency workers have discovered scores of bodies from at least three mass graves inside the BDR headquarters in Dhaka.
Among the bodies unearthed were those of Major-General Shakil Ahmed, the BDR commander, and his wife.
All had been shot dead and their bodies hurriedly dumped in sewers.
Al Jazeera's Nicolas Haque, reporting from Dhaka, quoted eyewitnesses as saying that it all started in the Bangladesh Rifles meeting hall, where officers and soldiers of the army and BDR had gathered for a celebration.
Trouble started when the BDR director general apprehended a border guard for entering the hall with a gun against the rules.
The incident provoked a collective walk out of the BDR soldiers, Haque said.
Witnesses said that thirty heavily armed border guards returned soon after dressed in fatigues, spraying the senior officials with a round of bullets, kicking off this two day bloodbath.
About 300 BDR troops have been arrested and thousands remain at large after fleeing the compound following the killings.
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.