The charges were read to him Thursday at the office of the Burundi’s chief prosecutor.
The former prime minister was arrested last week, following reports that he was on the run and his arrest was confirmed in a short statement released by the chief prosecutor.
"Alain Guillaume Bunyoni is currently in the hands of the police," read the statement signed by General Prosecutor Sylvestre Nyandwi.
Bunyoni’s family has accused the government of kidnapping him.
"Kidnap someone without a warrant and call it an arrest? Shame! Unless it was intentional," his daughter Darlene Bunyoni said in a Twitter post. She added that the arrest is "laughable and embarrassing for everyone involved in the handling of this matter."
On Monday, Agnes Bangiricenge, the spokesperson of the office of the chief prosecutor, told a news conference that Bunyoni was accused of threatening national security, the good functioning of the national economy and illegally receiving interest.
Bunyoni's family say they fear he may have been tortured while in custody, having not seen him since his arrest.
Speaking to VOA’s Central Africa Service, Sixte Vigny Nimuraba, president of Burundi’s Human Rights Commission, denied allegations that Bunyoni has been tortured.
"I met him a day after his arrest. We were together again this Wednesday. He is doing very well. He is ready to appear before the court," Nimuraba said. "There is no issue at all about that. He is doing well. He has not suffered any act of torture or any other abuse since his arrest."
Nimuraba also confirmed reports that Bunyoni’s wife had been questioned by authorities.
Friend of Burundi's late president
Bunyoni was prime minister from June 2020 until September 2022, when he was removed from that position by Burundi's President Evariste Ndayishimiye.
He was among the most influential and powerful army generals in the ruling National Council for the Defense of Democracy - Forces for the Defense of Democracy party, or CNDD-FDD.
Until the unexpected death of former President Pierre Nkurunziza in June 2020, Bunyoni was considered the second most powerful person in the country and a close friend to Nkurunziza.
The firing of Bunyoni happened a week after Ndayishimiye warned that some unnamed people were plotting to overthrow his government and sabotaging it.
Bunyoni has been under U.S. sanctions since 2015 for allegedly committing human rights violations during the violent crackdown that followed the decision by Nkurunziza to seek a controversial third term.
Human Rights Watch (HRW), which has documented rights abuses in Burundi, says the arrest of Bunyoni is an opportunity for justice in Burundi.
"The arrest of Burundi’s former Prime Minister Alain Guillaume Bunyoni is certainly a chance for justice in Burundi. But it should be followed by a full judicial investigation of abuses committed by security forces during his time as minister for public security from 2015 to 2020," said Clementine de Montjoye, a researcher in the Africa division at HRW.
"At the time," she added, "Human Rights Watch documented how police killed and tortured suspected government opponents, including the violent crackdown that began in 2015. There is no indication so far that the criminal abuses by police during this time are also being investigated at this moment."
Montjoye says decisions to prosecute should be made based on evidence following a full and independent criminal investigation.
"We are calling for the process to be transparent and credible and for Bunyoni to be given a fair trial in the presence of independent monitors and be treated according to established legal rules and principles," she said.
In a statement, Amnesty International said the arrest of Bunyoni should serve as an opportunity for accountability but also raised concerns around his arrest.
"The lack of transparency around the arrests and detention is worrying. Authorities must ensure that those arrested are immediately allowed access to their lawyers and family visits. Authorities must also ensure that their rights to a fair trial, and rights to freedom from torture and other ill-treatment, are fully respected," Flavia Mwangovya, Amnesty International’s deputy regional director, said in a statement.
Bunyoni’s daughter Darlene accused the government of holding her family hostage in a Twitter post.
Mwangovya called on the government of Burundi to refrain from reprisals against Bunyoni’s family, who she says were reportedly held incommunicado in their house for five days.
"Unless family members are also targeted by the investigation, there is no legitimate reason why they should not be allowed to move and communicate freely," she wrote.
Burundi’s Ministry of Justice and the office of the prosecutor did not respond to a request from VOA for reaction to the allegations made by Bunyoni's daughter and human rights organizations.
This story originated in VOA’s Central Africa Service. Venuste Nshimiyimana in London contributed to this story.