Faisal Arefin Dipan, who ran 'Jagriti Prokashony', was hacked to death in his office on the second floor of Aziz Supermarket at Shahbagh on Saturday, blogger and online activist Mahmudul Haque Munshi told bdnews24.com.
Dipan was attacked hours after another publisher Ahmedur Rashid Tutul was attacked with sharp weapons.
He was declared dead by doctors after being taken to Dhaka Medical College Hospital (DMCH), police said.
Tutul is being treated at DMCH along with writer Ranadipam Basu and blogger Tarek Rahim, who were also injured in the attack.
Tutul, who owns publishing house ‘Shuddhaswar’, was hacked up in his office at Lalmatia around 2:30pm along with blogger Rahim and writer Basu.
Doctors said Tutul and Rahim were in critical condition.
Later, DMP Commissioner Asaduzzaman Mia, quoting doctors, said all the three were out of danger.
'Shuddhaswar' had published a number of books written by Avijit Roy.
Faisal Arefin Dipan was the only son of well-known writer and professor of Dhaka University’s Bengali department Abul Kashem Fazlul Haque.
His 'Jagriti Prokashony' had published Avijit Roy's popular title ‘Biswaser Virus’ (Virus of Faith).
The book was a hit with rationalists and freethinkers, but it had upset the Islamist radicals, who are suspected to be involved in his murder.
Roy was murdered by machete-wielding killers on the Dhaka University campus in February this year during the Amar Ekushey Book Fair.
Son of well-known physicist Ajoy Roy, Avijit was an US citizen but a passionate blogger and writer who promoted rationality and science.
Dipan was a classmate of Avijit at Udayan School. He studied economics at Dhaka University. His wife is a doctor. He left behind two children.
Aziz Supermarket Traders Association General Secretary Morsalin Ahmed said the shops at the market were closed after the news of the attack on Dipan broke in the evening.
Dipan’s father Professor Haque said the publisher had left home for office around 1:30pm.
No one received the call on his mobile phone when the family tried to reach him around 4:30pm, he said.
The Dhaka University teacher said he went to the office after around an hour and found his son ‘beheaded’.
He suspects that Dipan was killed for publishing Avijit’s books.
“He had no enemies. They have attacked others who published Avijit’s books. So it is natural to presume that they have also killed my son,” he said.
Though no group has claimed responsibility for the serial attacks on the two publishers on Saturday, bloggers and online activists are blaming Islamist radicals for them.
Dhaka police spokesperson Muntasirul Islam told bdnews24.com that Dipan's was a 'pre-planned murder.'
"It seems more than one assassin were involved in the murder."
Like during previous attacks on secular bloggers, Saturday's attacks on the two publishers were also carried out with sharp weapons.
Dhaka Metropolitan Police (Ramna Zone) ADC Mohammad Jashim told bdnews24.com that Dipan was rushed to the hospital around 6pm after the attack, with blood all over his body.
Doctors declared him dead soon after.
'Jagriti Prokashony' employee Md Alauddin told bdnews24.com: "When I entered the office around 5:30pm, Dipan was lying in a pool of blood. There were deep cuts on his neck and upper shoulder."
Saturday's serial attacks on the two publishers have raised the heckles in Bangladesh's huge fraternity of secular thinkers and intellectuals.
Film maker and writer Shahriar Kabir denounced the attacks.
"These assassinations remind us of the killings of Bengali intellectuals by the Pakistanis. The same fundamentalist forces are attacking our free thinkers now. We must fight them with all we have."
Some secular groups also blamed the government for failing to provide protection.
Ganajagaran Mancha spokesperson Imran H Sarker said these attacks prove the "law enforcing agencies have totally failed".
"It is also not possible to carry out these attacks without connivance of some in the government," Sarker told reporters at Dhaka Medical College Hospital.