S.M. Abdur Rashid of the Second Additional Metropolitan Sessions Judge's court gave the order Thursday, bdnews24.com reported.
The explosion ripped through the second floor of a dormitory at the Jamayetul-Ulum-Al Islamia madrasa in Chittagong run by Izahar Oct 7 last year.
Izahar is also chief of hardline political outfit the Islami Oikya Jote.
Five students were injured, three of whom later died.
Izahar's son Harun was in charge of the dormitory. It tried to pass off the incident as a "laptop-explosion" but police had recovered handmade bombs, acid and explosives during a raid on the madrasa.
Police lodged three cases over the blast -- two under Explosives Act and the other for murder.