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.”

Ms. Díaz said the police pressured her to waive the right to an autopsy on her son, José Adán Bones, and she agreed because she was grieving and thought she would not be able to afford the forensic exam.

On Thursday, the Organization of American States said the Nicaraguan government had denied its request to conduct an on-site investigation into the killings. The organization’s Inter-American Commission on Human Rights said it would continue to investigate the deaths, as well as allegations that injured protesters were denied medical care and that the relatives of the those killed had to agree not to file complaints in exchange for receiving their loved one’s bodies.

The uprising began on April 19, led by university students in Managua protesting against an unpopular social security decree that would have forced workers to pay more and retirees to receive less. The students were already worked up over a fire at a nature reserve that the government had failed to control.

The response to the crackdown was intense, and the protests quickly broadened to encompass a much wider set of grievances with the Ortega couple’s rule and the steadily increasing concentration of power in their hands. Even government concessions, including the rescinding of the social security reform, did not quell the unrest.

Protesters turned out around the country, blasting the president’s control of the Supreme Court, the National Assembly and the elections council. The violence escalated when the student protests were met not just by the riot police, but also by swarms of young men in white and pink T-shirts declaring their membership in the Sandinista Youth — a pro-government organization that has been harassing demonstrators and sometimes throwing stones at them. Videos showed the police handing the young men rocks.

The vice president’s office, which controls news media access, did not respond to repeated messages seeking comment. But Bayardo Arce, one of the original Sandinista commanders and a top adviser to Mr. Ortega, acknowledged in an interview with Univision that the police “lost control” during the protests.

Protests even spread to longtime strongholds of Mr. Ortega’s Sandinista movement, with some demanding the president’s resignation and setting fire to government buildings. Two government sympathizers died blowing up an opposition radio station in León, according to the station owner and the Nicaraguan Center for Human Rights. A reporter was shot while recording a Facebook Live segment on Nicaragua’s northern coast, the video showed.

Vilma Núñez, formerly a Sandinista, founded the center, which has chronicled abuses by Mr. Ortega’s government. By her tally, 45 people have died so far in the unrest — 24 students, two police officers, a reporter and 18 others.

“They didn’t just use the police here,” she said. “They used strike forces.”

“The order was definitely to kill,” Ms. Núñez added, “not to stop the protest.”

Ms. Murillo, who is also vice president, blamed the students for the bloodshed. She said some people were killed by shotguns fired from inside the Polytechnic University, a focal point for the protesters, and accused the opposition of disseminating “fake news” by exaggerating the number of killings.

“Those tiny, petty, mediocre beings, those beings full of hate, still have the nerve to invent dead,” Ms. Murillo said in an address shortly after the unrest erupted, referring to the protesters. “For those crimes, we demand punishment,” she said.

Mr. Ortega was president during the 1980s, when the United States financed a war aimed at ousting him. He agreed to elections in 1990 and lost, but then returned to office in 2007 after he maneuvered changes to an election law that allowed him to take office with less than 50 percent of the vote.

Since then, he has faced international condemnation for chipping away at democracy. In 2008, he was accused of orchestrating rampant voter fraud in municipal elections, which gave him control of cities around the country. He stacked the Supreme Court and used that majority to get rid of the constitutional ban on term limits. He used legal ploys to eliminate opposition parties, and took control of most of the country’s television stations. All of this fed the resentment that boiled over into the current uprising.

Mr. Ortega’s socialist Sandinista Front party said several members of the Sandinista Youth had died in the unrest. The party defended the police, saying they acted prudently because “the destruction of the country could not be allowed.”

Opposition members fear the killings will become another example of impunity in Central America, where a number of governments have never been held to account for crimes over the past several decades.

Now the families of the dead must rely on the police, prosecutors and the judiciary — all firmly under Mr. Ortega’s control — to investigate.

In an annual report, the Permanent Committee on Human Rights showed photos of prominent law enforcement authorities, including the chief of the Supreme Court, waving the black-and-red Sandinista flag.

That, said the group’s leader, Marco Carmona, does not exactly inspire confidence.

“We cannot trust that there will be an objective investigation, a professional investigation, nor can we trust that the judicial authorities are going to be faithful in their application of the law,” said Denis Darce, who runs training projects at Mr. Carmona’s group. “Citizens will be practically defenseless.”

Mr. Bones, the young man who was killed, lived outside Managua and was visiting relatives in the capital when he went missing for several days. His bullet-riddled body suddenly appeared at a hospital morgue near one of the protest sites, where he apparently got caught in the cross-fire.

“They didn’t ask us any questions about him because they already knew how he died. They knew those shots came from them,” his sister, Migdalia Bones, said of the police. “Then a man at the hospital came up to me and whispered: ‘Go to the human rights office.’”

Because his body did not appear for days after the protests and his family has not made the trek to Managua to file official complaints with human rights agencies, Mr. Bones’s name does not appear on the official list of the dead that rights groups have compiled.

Even as bodies were buried without autopsies, the attorney general’s office held a news conference asking families to file written complaints and present any evidence they had.

“This has been handled in a way that is cruel and perverse,” said Ms. Núñez, the founder of the Nicaraguan Center for Human Rights. Next, she said, the government will start rounding up innocent people so authorities can appear to be working on the cases.

“Now comes the witch hunt,” she said.

The National Assembly, which is controlled by the Sandinista Front party, said it had formed a truth commission. The government Office for the Defense of Human Rights has also created a “victims committee” to record complaints.

On Monday, the government held a “peace and dialogue” rally to prove it has supporters, too, using the motto of the Sandinista Party to promote peace talks led by the Catholic Church.

“Where are these 63 dead? I have seen like 12 or 15. Let’s say there were 20; I haven’t seen them,” said Leonardo Loáisiga, 50, an attendee, referring to one widely cited, unconfirmed death toll. “Show me those 63 dead.”

But the killings have also soured some loyal Sandinistas like Ms. Díaz and the family of 16-year-old Jesner Josué Rivas, who died in the turmoil.

“Nicaragua is being left without university students because the government of Nicaragua is killing them,” said Norlan Rodríguez, whose nephew Jesner died a few blocks from a store that was being looted. “I am a Sandinista, and have been so since I was a little kid. But they killed my boy and I will never give those people my vote again.”