Harun Izhar, son of Hefajat-e Islam Nayeb-e-Ameer Mufti Izharul Islam Chowdhury, was arrested along with his bodyguard early yesterday, police say.
Harun, who is Hefajat's publicity secretary, is one of the prime accused in the cases filed over the explosion at Jamiatul Ulum Al Islamia Madrasa in Chittagong on Monday morning.
Also yesterday, Jubair Ahmed, 22, a student of the madrasa, who suffered 80 percent burns in the blast, passed away at Chittagong Medical College Hospital around 6:00am.
Habibur Rahman, 24, another injured, died at the hospital on Tuesday.
At least seven were wounded in the incident.
Police filed two cases -- one under explosive substances act and another for stashing acid -- accusing 12 identified and many unnamed persons.  Mufti Izharul and Harun were made the prime accused in both the cases.
A murder case was also filed last night against seven, including the father and son and one of the injured, Nurun Nabi.
Nurun Nabi, a diploma engineer, is also a charge-sheeted accused in a murder case filed for the killing of two people in a gunfight that took place in Chittagong after the war crimes verdict against Sayedee, police say.
He landed in jail on March 31 and got bail on May 22.
Now under treatment at Dhaka Medical College Hospital with 90 percent burns, he is a cadre of Islami Chhatra Shibir, according to police.
On Tuesday, talking to the media, CMP Commissioner Shafiqur Rahman said Nurun Nabi might have been taken to the madrasa for making bombs.
Police have recovered four hand-made grenades from the dormitory room where the blast happened. Eighteen bottles of picric acid, a bomb-making material, have also been found in Izharul's office.
Mufti Izharul, the founder and principal of the madrasa, has remained absconding since Monday evening.
Sources said acting on a tip-off, a joint team of Chittagong Metropolitan Police began a raid in Ichhapur village under Hathazari upazila around 1:00am yesterday.
Hathazari is known as the base of Hefajat, a radical Islamist organisation.
Police arrested Harun and his bodyguard Junaid, 30, in Ichhapur around 3:00am, said CMP Additional Commissioner Banaj Kumar Majumder.
During interrogation, Junaid claimed to be the security guard of the madrasa, said the police official.
Harun left the madrasa after the explosion and was hiding in his in-laws' house, from where he was detained, police said in a press briefing.
Several students of the madrasa and witnesses said Harun had arranged sending the injured to hospitals.
Harun, also deputy principal of the madrasa, along with two of his associates was arrested by detectives in the madrasa in November 2009 over his alleged links to the militant outfit Lashkar-e-Taiba (LeT).
Yesterday afternoon, a Chittagong court placed him on a 10-day remand in the two cases.
The court of Chittagong Metropolitan Magistrate Mashfiqul Islam passed the order when police produced Harun and six other arrestees with a prayer for remand.
One of the arrestees, Monir Hossain, was placed on a day's remand while each of five others, including Junaid, was put on a three-day remand in the explosives case.
Monir, hostel superintendent of the madrasa; its teachers Md Ishaq, Abdul Mannan and Tafsir Ahmed and a student named Habibur Rahman were arrested at the madrasa on Monday night.