Prosecutor's spokeswoman Julia Barrera confirmed the detentions of Social Welfare Secretary Carlos Rodas, Deputy Secretary Anahi Keller and shelter director Santos Torres on suspicion of homicide, mistreatment of minors and failure to fulfill duty.
Earlier in the day President Jimmy Morales said he had fired the chain of command at the country's child welfare agency, but did not specify how many employees were dismissed.
He also said his government has asked the FBI to help in the investigation of Wednesday's disaster.
Authorities have said the fire that swept through parts of the institution began when mattresses were set ablaze during a protest by residents protesting conditions at the overcrowded youth shelter. Some of the victims had escaped earlier, fleeing poor food and mistreatment, but were caught and confined at the facility.
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De Leon said last week that younger children fled the shelter because they were being abused by older residents.
In 2013, a 14-year-old girl was strangled by another resident at the shelter, investigators said.
Prosecutors say they are also investigating whether children were trafficked through the home for prostitution.
Four of the burn victims were flown to the Shriners Hospital for Children in Galveston, Texas, on Saturday. Morales' office said the Shriners Hospitals had arranged for their transfer.