The inquiry marks the first time the federal government has overseen a child abuse investigation. It was launched by Minister for Women and Child Development Renuka Chowdhury, whose ministry in April released a study that found more than half of children in India are sexually abused.
Chowdhury told reporters that the boy was sodomized daily for three months last year, and that justice was long overdue.
"The parents have been running from pillar to post," Chowdhury said. "I can't sit back and pretend it's not happening."
The boy's parents discovered the abuse after he fell sick and they took him to the hospital, where doctors determined that he was being abused, Chowdhury said.
Two of the men have been arrested, but police are still searching for the third employee.
Chowdhury said that the federal inquiry would run alongside the existing police investigation.
The federal investigation will deliver its report to her in two weeks, she added.
"I want a thorough investigation and I want to know where the system failed."
More than 53 percent of children in India are sexually abused, but most don't report the assaults, according to the April study. It was the first-ever national-level study, covering 13 of India's 28 states with a sample size of 12,447 children in the 5-12 age group, and 2,324 young adults.
Chowdhury's office is working on a new children's rights law to stiffen punishment against offenders.