The Bolivar Commercial reports that the order from U.S. District Judge Glen H. Davidson cites East Side High School and D.M. Smith Middle School.
The desegregation case dates back to 1965 when plaintiffs sued the Bolivar County school system, including Cleveland, to end white only and black-only schools.
The school system has been under the federal courts oversight ever since.
In 1989, the U.S. Department of Justice alleged that the Cleveland School District was still segregated.
In 1992, the district and government agreed that a magnet school program should be implemented at the junior high level to eliminate the "continuing racial identifiability of both Margaret Green Junior High and Eastwood Junior High (D.M. Smith)"
In 1995, the district was ordered to submit a plan to establish a high school level magnet program.
The government has been conducting a periodic review of the school system since 2006.
In 2011, the school district petitioned the court to remove it from federal oversight.
Davidson said in his order that if the government and the school district cannot agree on a plan by May 15, he will scheduled a hearing.
In the mid- to late-1960s, school districts across the South were sued for discrimination and given desegregation orders, which put them under the scrutiny of the Justice Department. A dozen or more school systems in Mississippi have petitioned the federal courts to come out from under such orders.