43-year-old Faisal Arefin Dipan was killed by terrorists in his office in Dhaka in 2015.
A renegade Bangladeshi army major who later became a terrorist leader has emerged as the key accused in the murder of a noted progressive publisher three years ago even as police today said they had finished their investigation in the case.
"Sacked and fugitive major Syed Ziaul Haq appeared to be the mastermind of the killing of publisher Faisal Arefin Dipan in our investigation," a spokesman of police's detective branch said.
He said seven other operatives of the banned Ansarullah Bangla Team (ABT) were also named in the charge sheet but Zia and another assailant were still on the run while others were in jail to face trial in the case.
The spokesman said the case was filed under the anti-terrorism law which requires police to obtain home ministry approval.
The terrorists had murdered 43-year-old Dipan in his office in central Dhaka's Shahbagh area in 2015, months after they killed atheist blogger Avijit Roy, the first victim in a wave of violence against secular writers, religious minorities and foreigners in Bangladesh.
Bangladesh had earlier announced a bounty of 20 lakh Takas for Zia's capture.
The police said Zia was the banned outfit's "operational chief" while he was on the run since 2011 when he allegedly tried to orchestrate a pro-Islamic army coup.
The latest development comes five months after a special court in Dhaka handed down the death penalty to two terrorists, two years after they hacked to death a professor in Rajshahi University in northwestern Bangladesh.
Operatives of Jamaatul Mujahideen Bangladesh (JMB) - said to be allied to the Islamic State - hacked 58-year-old Rezaul Karim to death using machetes near his house in Rajshahi city.
Police have recently intensified investigations into a series of clandestine attacks on secularists and liberal intellectuals, bloggers and minorities, including gay activists.
Top secular writer and physicist professor Jafor Iqbal was the last such target of terrorists in March this year when he narrowly survived an attack on the campus of the Shahjalal Science University in northeastern Sylhet.