Shayek Abdur Rahman has admitted that his outlawed Jamaat-ul-Mujahideen group was mainly responsible for the explosion of hundreds of small bombs since August 2005, Lieutenant Colonel Gulzaruddin Ahmed, intelligence chief of the elite Rapid Action Battalion (RAB) force, said on Friday.
At least 30 people were killed and over 150 wounded in the attacks, which created panic across the country.
Shayek, supreme leader of the Jamaat-ul-Mujahideen, was captured in the northeastern town of Sylhet on 2 March following a siege of the house where he lived with his family.
Formal charges against Shayek, which may include sedition and murder, will be laid later, officials said. He could face the death penalty if convicted.
Shayek has already been sentenced to 40 years in prison while in hiding for his role in the killing of two judges in January in southern Jhalakathi town.
Last Monday, another of Bangladesh's most wanted militants, Siddikul Islam Bangla Bhai, was captured during a gun battle in the northern district of Mymensingh.
Wounded in the battle, Bangla Bhai, chief of another outlawed group called Jagrata Muslim Janata Bangladesh, is now being treated at an armed forces hospital in Dhaka.
Security officials said on Friday his condition was improving and he would be fit for questioning in a few days.
The two groups are fighting for introduction of sharia law in Bangladesh, a mainly Muslim democracy.