MANAGUA, Nicaragua — It has been two weeks since lethal clashes between protesters and pro-government forces erupted in Nicaragua, and the number of deaths is still not clear. But this much is: It keeps climbing.

By Friday, the toll of students, counterprotesters, bystanders and police officers who died in five days of student-led demonstrations against President Daniel Ortega’s government had risen to at least 45 and was expected to climb further. In this Central American country of six million people, that tally makes this the deadliest unrest by far since nearly three decades of war ended in 1990.

Government agencies tightly controlled by Mr. Ortega and his wife, Rosario Murillo, have vowed to set up truth commissions and investigations. The question of whether anyone ordered the killings is poised to become a major issue in coming peace talks between the government, the Catholic Church, the business sector and the university students. The challenge is the most critical threat to Mr. Ortega’s presidency since he was re-elected in 2007.

“He has two options: dead or alive,” Rosa Díaz said of Mr. Ortega after her 29-year-old son’s dead body turned up at a hospital following a particularly brutal night of protests in the capital, Managua. “But he has to leave office.”