Authorities also announced the indefinite closure of all public and private universities from Wednesday following the protests over public sector job quotas, which include a 30 per cent reservation for family members of fighters from the 1971 war of independence from Pakistan.
Later, Prime Minister Sheikh Hasina said the government will form a judicial committee to investigate the killings.
Wednesday's violence broke out after security forces deployed outside the Dhaka University campus as students chanted: "We will not let our brothers' blood go in vain".
Protesters in Dhaka have rallied against public sector job quotas they view as being unfair. (EPA PHOTO)
Police fired tear gas and rubber bullets and lobbed sound grenades at the students as they marched in processions carrying coffins in solidarity with those killed, protest co-ordinator Nahid Islam said.
The quotas have caused anger among students who face high youth unemployment rates, with nearly 32 million young Bangladeshis not in work or education out of a total population of 170 million people.
Demonstrations intensified after Hasina, the daughter of Sheikh Mujibur Rahman, who led Bangladesh's independence from Pakistan, refused to meet the protesters' demands.
The protests turned violent this week when thousands of anti-quota protesters clashed with members of the student wing of the ruling Awami League party across the country.Â
Six people, including at least three students, were killed during clashes on Tuesday, police said.
Prior to the killings, she had labelled those opposing the quota as "razakar" - a term used for those who allegedly collaborated with the Pakistani army during the 1971 war.
But on Wednesday she said in an address: "I believe our students will get justice. They will not be disappointed."
Announcing a judicial investigation, she assured families of those killed of her full support.
The protests are the first significant challenge to Hasina's government since she secured a fourth consecutive term in January in an election boycotted by the opposition Bangladesh Nationalist Party (BNP).
Experts attribute the unrest to stagnant job growth in the private sector as opposed to government jobs, which offer regular wage hikes and other privileges.
Violence was also reported in many other places across the country, with students blocking a bridge, leaving a 10km-long tailback of vehicles.
Police said they had to fire tear gas to disperse stone-throwing BNP activists during a protest in Dhaka.