The protests came a day after secular publisher Faisal Arefin Dipan, 43, was killed in his third-floor office in central Dhaka.
Ahmedur Rashid Tutul, a publisher who worked with slain atheist writer and blogger Avijit Roy and bloggers Ranadipam Basu, 50, and Tareque Rahim, 30, were hacked by unidentified assailants in a separate incident.
A group identifying itself as Ansar al-Islam -- Bangladesh chapter of al-Qaeda in Indian Subcontinent (AQIS) -- claimed responsibility for the attacks.
Home Minister Asaduzzaman Kamal said the attacks on publishers and bloggers were "isolated incidents".
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Speaking to reporters, he claimed the country's law and order situation was all right.
Asked why such incidents were taking place repeatedly, Kamal said, "Such isolated incidents occur in other countries as well."
Dhaka Metropolitan Police (DMP) Joint Commissioner Monirul Islam said that the police is investigating the claims made by Ansar al-Islam, a militant group suspected to be under the banned Ansarullah Bangla Team umbrella.
When asked if such targeted attacks can be prevented, he said, "Visible policing is not enough to prevent such incidents. We need a special counter terrorism unit which we don't have."
In primary investigation, he said, it is evident that the attackers are not trained killers.
"We cannot say for sure if this attack on the publishers is related to the previous attacks on bloggers without further investigation," he said.
Another leading publisher Farid Ahmed today alleged unidentified assailants sent him an SMS issuing a death threat for publishing books authored by "atheists".