After James P. Coleman won Mississippi's gubernatorial election in 1955, he proposed to the Legal Educational Advisory Committee the creation of "a permanent authority for maintenance of racial segregation with a full staff and funds for its operations to come out of tax money.

While most legislators and the local media were supportive of the bill, some representatives were skeptical of its power to give funds to private entities, fearing that the body would essentially become a partner of Citizens' Councils, civic groups organized to block desegregation.

[9] Other principal investigators for the Sovereignty Commission were Virgil Downing, Leland Cole, Fulton Tutor, Edgar C. Fortenberry, and James "Mack" Mohead.

[11] As the state's public relations campaign failed to dampen rising civil rights activism, the commission put people to work as a de facto intelligence organization, trying to identify citizens who might be supporting civil rights initiatives, be allied with communists, or whose associations, activities, and travels did not seem to conform to segregationist norms.

Swept up on lists of people under suspicion by such broad criteria were tens of thousands of African-American and white professionals, teachers, and government workers in agricultural and other agencies, churches, and community organizations.

The "commission penetrated most of the major civil rights organizations in Mississippi, even planting clerical workers in the offices of activist attorneys.

[18]: 75 The commission also used its intelligence-gathering capabilities to assist in the defense of Byron De La Beckwith, the murderer of Medgar Evers in 1963, during his second trial in 1964.

[18]: 204–5 In 1964, the Sov-Com passed on information regarding civil rights workers James Chaney, Michael Schwerner, and Andrew Goodman, to the conspirators in their murders during Freedom Summer.

During his tenure the commission enlarged its investigative operations, sending agents across the state to report on civil rights activities.

It also surveyed literature and libraries and collected information on persons viewed to be expressing liberal ideas or violating traditional racial mores.

[21] During his tenure, the agency director, Erle Johnston, owner of The Scott County Times, expanded the public relations role.

He tried to form closer ties with business while monitoring proclaimed subversive groups, such as the Congress of Racial Equality, founded by James Farmer.

After a requirement was attached to a state appropriations bill in June 1966 that the commission formally convene before receiving any money, the agency's leadership met on August 8, formally adopting a policy declaring the commission as a "watch dog over subversive individuals and organizations that advocate civil disobedience; as a public relations agency for the state; and as an advisor for local communities on problems resulting from federal laws or court orders.

"[21] During Johnson's tenure the commission continued to monitor individuals and groups who challenged racial norms and provided advice to other government officials on ways to work around the Civil Rights Act of 1964.

He paid more direct attention to the commission than his predecessor, regularly convening meetings of its members and typically attending them in person.

"[21] During this time the commission followed up on requests from local officials to investigate civil rights-related activities and examined drug use and disruptions on university campuses.

Both men demurred on making their allotted appointments to the commission and avoided attending its monthly meetings, sending representatives in their stead.