"The prime minister has announced amnesty for those involved in the trouble. We now hope to lay down our arms and go back to barracks," Mohammed Towhid, a spokesman for the mutineers, told reporters after the meeting.
But one military official confirmed the mutineers had yet to surrender.
"Efforts are still continuing to persuade the rebels to give up," the official, who did not want to be named, told reporters.
Nicolas Haque, Al Jazeera's correspondent in Dhaka, said the Rifles wanted confirmation they would not be attacked by the army.
"They announced on a speaker phone that they would not open the gates until they had a written statement from the prime minister that they would be pardoned, and a written statement from the army that they would not attack the compound they're in," he said.
For more than four hours intermittent gunshots rang out at the headquarters, while smoke billowed from the compound.
Guards reached inside the compound by phone said they were upset that their officers had not raised their demands for equal pay and working conditions as army soldiers when Hasina visited the headquarters the day before.
It was not immediately clear if the government would agree to all of their demands, which included more food rations and a chance to participate in lucrative, high-paying UN peacekeeping missions.
Kailash Budhwar, a London-based South Asia analyst, told Al Jazeera that the mutiny was "most unexpected".
"And it happened from a unit that was supposed to be most disciplined ... a paramilitary force who guard the border," Budhwar said.
"This certainly brings to memory the dark days when there was turmoil and anti-social takeover, and there are other undercurrents in Bangladesh who might take advantage of the situation," he said.
Bangladesh, an impoverished nation of 150 million people, has a history of military coups and political assassinations.
Two of the South Asian nation's leaders have been slain in military takeovers, and there have been 19 failed coup attempts since the country gained independence from Pakistan in 1971.
Hasina was elected as prime minister at the end of December after about two years of military rule in the country.