A Jamaat cadre was killed and 47 others were injured in a clash with police in Meherpur district while a commuter died after being attacked by picketers in Sirajganj Sadar upazila.
The right-wing party, however, claimed its another cadre died in the clashes.
Police said they opened fire when strikers attacked an officer with sharp objects in the district. The firing left one dead.
Other districts also witnessed vandalism, explosions and detention as the strike stepped into second consecutive day.
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A senior leader of Meherpur Jamaat unit said another party cadre, who was injured during the clash, succumbed on way to hospital. Besides, he said their 10 activists sustained bullet injuries during the clash.
Yesterday, one person was killed and several others injured in the violent protests.
The apex court on Tuesday sentenced Jamaat assistant secretary general Mollah to death, overruling the judgment of a special tribunal that had given him life term for war crimes committed during the country's 1971 liberation war.
This is the first such case which came for the apex court review while two war crimes tribunals are trying the high profile accused of "crimes against humanity" during the war, mostly belonging to Jamaat, which was opposed to the country's independence from Pakistan.
The two tribunals have already handed down death penalty to four and long term or life imprisonments to two others.
Officially three million people were killed in the liberation war during which Jamaat allegedly masterminded the murders of the country's leading intelligentsia including professors, doctors and journalists.