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Every high school, university and Islamic seminary around the country was told to remain shut until further notice following weeks of escalating demonstrations against civil service hiring policies.
Tuesday saw a significant escalation in violence as demonstrators and pro-government student groups attacked each other with hurled bricks and bamboo rods, and police dispersed rallies with tear gas and rubber bullets.
Education ministry spokesman M. A. Khair told AFP the shutdown order was issued for "the security of the students".
Khair later told AFP the order had been extended to include universities, where most students participating in the protests are enrolled.
At least six people were killed on Tuesday as demonstrators mobilised for another day in cities around the country, defying earlier calls by Prime Minister Sheikh Hasina and the supreme court to return to class.
Three died in Chittagong and had signs of bullet injuries, hospital director Mohammad Taslim Uddin told AFP, adding that another 35 had been injured during clashes in the port city.
Another two died in Dhaka, where rival student groups threw bricks at each other and blocked roads in several key locations that ground traffic to a halt in the megacity of 20 million.
Police inspector Bacchu Mia confirmed the deaths to AFP, saying one had succumbed to head injuries, while at least 60 people were also injured.
In the northern city of Rangpur, police commissioner Mohammad Moniruzzaman told AFP that a student had also been killed in clashes there.
He did not give details as to how the student died, but said police had fired rubber bullets and tear gas to disperse protesters.
Rangpur Medical College hospital director Yunus Ali said the "student was brought dead to the hospital by other students".
Tauhidul Haque Siam, a student reporter from the city's Rokeya University, told AFP that ruling party supporters had attacked anti-quota protesters, while police fired rubber pellets from shotguns.
"Police opened fire from their shotguns on the protesters," Siam said, adding he had been injured.
He said the dead student had been "killed in the firing", but it was not possible to independently verify his account.
As the day wore on and with some key highways around the country blocked by the protesters, authorities deployed the paramilitary Border Guard Bangladesh (BGB) force in five major cities including Dhaka and Chittagong.
UN Secretary-General Antonio Guterres called on the government in Bangladesh "to protect the demonstrators against any form of threat or violence," according to his spokesman Stephane Dujarric.
"It is a fundamental human right to be able to demonstrate peacefully and government should protect those rights," Guterres said, according to the spokesman.
- 'Violence against peaceful protesters' -
Tuesday's clashes came a day after confrontations between anti-quota demonstrators and members of the ruling Awami League's student wing that left more than 400 people injured in Dhaka.
"We are not here to do violence," one protester in Dhaka, who declined to give their name for fear of reprisal, told AFP.
"We simply want our rights. But the ruling party goons are attacking our peaceful protests."
Near-daily marches this month have demanded an end to a quota system that reserves more than half of civil service posts for specific groups, including children of veterans from the country's 1971 liberation war against Pakistan.
Critics say the scheme benefits children of pro-government groups that back Prime Minister Sheikh Hasina, 76, who won her fourth consecutive election in January after a vote without genuine opposition.
Amnesty International afterward urged Bangladesh to "immediately guarantee the safety of all peaceful protesters".
US State Department spokesman Matthew Miller also denounced the "violence against peaceful protesters", prompting a rebuke from Bangladesh's foreign ministry.
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