Avijit Roy, an US citizen of Bangladeshi origin, was killed by unknown attackers on Thursday night. He had received numerous death threats from Islamist militant groups.
More than 1,000 mourners gathered to pay respects and lay wreaths on Roy's coffin which has been placed inside Dhaka University, a bastion of secularism and free speech in the Muslim-majority nation.
"It's a heinous murder. My question is, why did it take place?" Kamal Hossain, the architect of Bangladesh's secular constitution, told reporters as Roy's father stood by.
"Avijit was killed because of his writing. By killing him, the killers have torn apart our constitution," he said.
Protesters also gathered at the spot where Roy was killed inside the university's sprawling campus, demanding the immediate arrest of his attackers.
The attack on Roy, founder of the Mukto-Mona (Free-mind) blog, as he left a book fair also seriously injured his wife.
Roy is the second Bangladeshi atheist blogger to have been murdered in two years and the fourth writer to have been attacked since 2004.
No one has yet claimed responsibility for the attack, which has shocked many in a country already reeling from weeks of violent political protest.
Police have launched an investigation and recovered the machetes used in the attack, which they compared to a fatal assault on atheist blogger Ahmed Rajib Haider in 2013.
Cultural activists, left-wing students, bloggers and members of secular groups were among those who came to honour the slain author, whose anti-religion books and blogs infuriated Bangladesh's hardline Islamist groups.
The United States has condemned the murder as a "shocking act of violence".
Ajoy Roy stood alongside his son's coffin as mourners filed past.
He reiterated that Islamist militants were responsible for his son's death, but also blamed the government for failing to protect him despite repeated threats on his life.
"I am speechless at this moment of mourning. When the fundamentalists threatened, I informed the Inspector General of Police and Deputy Inspector General of Police," Ajoy Roy said.
"This murder has proved their utter failure."
Source: AFP, via I-Net Bridge
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