Branch identified the deputies as Anthony Thompson, who runs the jail, and Darryl McPhatter, a detective with the criminal investigations unit.
Branch declined to comment further about what the internal investigation found that prompted the suspensions. He also would not say whether the internal investigation was the one launched after Hania Aguilar's body was found.
Aguilar, 13, was kidnapped from outside her home Nov. 5 as she waited to go to school. Twenty-two days later, she was found dead in Robeson County.
Michael Ray McLellan faces charges of first-degree murder, first-degree rape, kidnapping, and more in connection to Aguilar's case.
Robeson County District Attorney Johnson Britt said McLellan should have been behind bars in 2018 and never had a chance to harm Aguilar.
Britt said in 2017 DNA from the 2016 rape kit named McLellan as a possible match. Britt said the Robeson County Sheriff's Office was notified.
"That would've given them probable cause to get a search warrant to obtain a known DNA sample from McLellan," Britt said.
That never happened.
"In all likelihood, had (the 2016 rape investigation) gone forward and we established a case against (McLellan) at that time, Hania would not have died," Britt said.
After Britt's comments, Robeson County Sheriff's Office launched an internal investigation into what happened with the 2016 case.
Newly elected Robeson County Sheriff Burnis Wilkins said in a statement on Dec. 13 that an investigation had begun within the Internal Affairs Division "regarding this serious matter brought forth by the Robeson County District Attorney's Office."
"We're going to be transparent here, there's nothing going to be hidden, we're going to get to the bottom of it," Wilkins said.
Now, two Robeson County deputies are suspended. The sheriff's office has not officially commented on the exact circumstances surrounding the suspensions.
NEW AT 6: The family of Hania Aguilar in court today. Murder suspect, Michael Ray McLellan was not. I’ll explain why, plus the major shakeup in the Robeson County Sheriffs Office amid an internal investigation. #abc11 pic.twitter.com/aGLfS3Ls9J— Morgan Norwood (@MorganABC11) December 21, 2018
McClellan was not at his court appearance Friday, but a judge granted his attorney's request for more time to review the evidence. For safety reasons, McClellen has been moved to Central Prison in Raleigh.