The recusals come less than a week before the two-year anniversary of the discovery of Johnson's body in the center of a rolled gym mat in the old gym at Lowndes High School on January 11, 2013.
Johnson's parents, Kenneth and Jacquelyn Johnson, said they never believed investigators' conclusion that their 17-year-old son died while struggling to reach for a shoe at the center of the mat. They believe their son was murdered.
Months after an autopsy conducted by the state medical examiner supported the local investigators' conclusion, Johnson's parents hired a pathologist, who said he found evidence of unexplained, nonaccidental blunt force trauma to Johnson's neck.
In June 2013, attorneys representing Kenneth and Jacquelyn Johnson sued the Lowndes County Sheriff's Office to get access to the department's full investigative file and a copy of school surveillance video recorded around the time Johnson disappeared. According to the lawsuit, the department's refusal to release the file was a violation of Georgia's Open Records Law.
Chief Judge Harry Jay Altman II ordered the department to release the files and video several days after CNN joined the suit in October 2013.
In November 2014, CNN filed a lawsuit against Lowndes County Schools to get access to clones of hard drives containing the original recordings of surveillance video given to sheriff's investigators. The lawsuit also claims the recordings are public record and the school's refusal to release them constitutes a violation of the state's Open Records Law.
The dispute has not yet been resolved.
"Given the fact that officials with whom the judges in the circuit deal with everyday are involved, it is not fair to the parties for any judge in this circuit to rule on contested matters of importance to the parties and the community," Altman wrote in a letter addressed to attorneys representing all parties.
Only five of the seven judges in Georgia's Southern Judicial Circuit hear cases regularly. Two senior judges hear cases only after special assignment.
"His decision cuts to the very heart of this matter, especially for this family. That is: Can they get fair and impartial people to look at what happened to this child and render a fair decision so they can have peace at night?" said Johnson's attorney, Benjamin Crump.
Altman had mediated requests for records in the case for more than 18 months before Thursday's recusal.
"While I had hoped that at least the preliminary matters would be dealt with through informal mediation, I do not see that happening," Altman wrote.
"The normal process for case assignment after judicial recusal will result in another judge being assigned to the case following which a hearing will be scheduled to decide the matters now before the Court," the Lowndes County Sheriff's Office's attorney Jim Elliott told CNN in a written statement.
An attorney representing Lowndes County Schools did not immediately respond to CNN's request for comment.
"Georgia is a big state. I think Atlanta is one of the major cities in America and I'm sure there are a lot of judges for them to choose from, not only in Atlanta but throughout the state of Georgia. The hope is that you will find a judge who is as fair and impartial," Crump said.