Steven Dettelbach, the U.S. attorney for the Northern District of Ohio, will leave his post on February 5 and return to private practice, according to the statement.
The federal criminal investigation will continue to be led out of the Northern District of Ohio, spokesman Michael Tobin said.
The probe was transferred to Dettelbach's office in November after Michael Moore, the U.S. attorney for the Middle District of Georgia, announced his resignation. Moore launched the federal investigation in October 2013 and now works for an Atlanta law firm.
Dettelbach's resignation comes after a high-profile civil rights attorney left the case.
Attorney Benjamin Crump, who has represented families in several high-profile civil rights cases, including those of Michael Brown and Trayvon Martin, is no longer representing Johnson's parents.
In an October 29 letter, Crump informed Jacquelyn and Kenneth Johnson that his firm would be unable to continue its legal representation in coordination with their lead attorney, Chevene King.
Crump says the State Bar of Georgia did not grant him special permission to represent the Johnsons beyond the initial pleadings to acquire surveillance recordings from Lowndes High School, where Johnson was found dead in January 2013.
"I have not been able to participate in any meaningful way with Attorney King in the strategy, the drafting or the filing of any pleadings in your son's wrongful death claim beyond that one initial pleading," Crump wrote.
The letter was submitted to Lowndes County Superior Court this month as part of a larger filing in the Johnsons' $100 million wrongful death lawsuit against dozens of local and state officials, along with former students and others.
In that filing, King wrote that Crump's departure came "without warning."
The general counsel for the State Bar of Georgia was not available for comment. However, Georgia law dictates that the court, not the State Bar, approve or deny an attorney's application to join a case.
The State Bar's general counsel expressed "no objection" to Crump's application to represent the Johnsons in the fight for surveillance video, according to a December 2013 letter to a Lowndes County judge, provided to CNN by the State Bar.
King told CNN he will expand the legal team but did not say when additional attorneys would join the case.
The Lowndes County Clerk of Court's office says there is no document on file that shows Crump applied to represent the Johnsons in the wrongful death case.
Several attempts to reach Crump were unsuccessful.
An accident or a homicide?
Johnson, 17, disappeared between classes at Lowndes High School on January 10, 2013. His body was found in a rolled gym mat the next day.
According to the Lowndes County Sheriff's Office, there were no witnesses. State and local investigators said Johnson died accidentally, after getting stuck in the mat while reaching for a shoe.
Johnson's parents later ordered an independent autopsy. A pathologist hired by Johnson's parents found evidence of "unexplained, apparent non-accidental blunt force trauma" to the teen's neck.
He said Johnson's death was the result of a homicide.