The main opposition Bangladesh Nationalist Party (BNP) and its Islamist allies called for a strike after saying that hundreds of people died on Sunday and early Monday, when police broke up a mass rally in central Dhaka.
According to an AFP tally compiled after talking to police and medical sources, 38 people are known to have been killed since Sunday afternoon when police first confronted Islamist activists who had blockaded the capital.
The Islamists are trying to pressure the government into introducing a new blasphemy law and have been calling for the execution of bloggers whom they accuse of having insulted the Prophet Mohammed.
A border guard succumbed to his head injuries Tuesday to raise the tally from Monday's 37, police inspector Mozammel Haq told AFP, adding dozens were still being treated in hospital.
The country's most prominent daily Prothom Alo said at least 49 people have died in the clashes, some of the fiercest street violence in decades. However, the BNP says the real number of dead runs into the "hundreds", accusing the authorities of concealing bodies but without giving any evidence.
"We have called two days of nationwide strike to protest the mass killing of Hefajat-e-Islam workers and supporters on Sunday and Monday," BNP spokesman Khandaker Mosharraf told AFP on Tuesday.
The strike will begin at 6:00 am (0100 GMT) on Wednesday and end at 6:00 pm on Thursday, Mosharraf added.
Police on Tuesday announced charges against 194 activists of the Hefajat-e-Islam (Protectorate of Islam), a hardline Islamic group behind the massive protests. Its secretary general Junayed Babu Nagori, who was detained on Monday night, faces a murder charge, police sub-inspector Tabibur Rahamn told AFP.
Hefajat's main leader, 90-year-old Allama Ahmad Shafi, was put on a plane to the country's second city Chittagong on Monday where his supporters clashed with police, leaving at least five people dead.
Information Minister Hasanul Haque Inu accused the heads of religious seminaries of encouraging "terrorist activities" by sending their students out to join the protests.
"The madrassa superintendents who are encouraging their students to take part in terrorist activities will be tried," he told a briefing.
Chanting "Atheists must be hanged", Hefajat activists marched along at least six highways on Sunday, effectively cutting Dhaka off from the rest of the country. Police said the number of protesters reached around 200,000 at one point.
The protest by Hefajat, which draws support from madrassas, was another sign of the divide between Islamists and the secular government, after the deaths of around 100 people earlier this year in violence linked to war crimes trials.
Three leading Islamists have so far been convicted by a special tribunal for their role in mass killings during the 1971 independence war, which saw what was then East Pakistan break from Islamabad.
The overall death toll in violence between religious hardliners and the police since January now stands at around 150.
UN Secretary-General Ban Ki-moon has called for an end to the violence, expressing his sadness at the loss of life. Ban "urges political and religious leaders to engage in constructive dialogue and help defuse the tensions", said UN spokesman Martin Nesirky.