In a brief address to the nation, Hasina said, "You surrender the arms. I'm giving you my word that none of you will be harmed. Otherwise, I'll be bound to take any step in the interest of the country".
"I am trying to solve the problems through negotiations, not through using force," she added.
Meanwhile, fresh gunshots were fired at the BDR headquarters in the capital at about 1:00 p.m., the Daily Star reports.
Several rounds of gunshot were fired inside the headquarters near its Jigtola gate.
The mutiny by paramilitary troops was reportedly spreading to other parts of the country.
Nearly 50 people are feared dead after paramilitary troops staged a mutiny on Wednesday morning at the headquarters of the Bangladesh Rifles in Dhaka over pay and career advancement conditions.
The Bangladesh Rifles (BDR) has 45,000 men stationed at 64 camps across the country.
Many of the dead are believed to be senior officers of the Bangladesh Rifles.
At least five bodies in Army uniform have been brought out of a marshy area within the BDR headquarter compound.