The Parchman investigation, which began in February 2020, is one of several major prison inquiries undertaken or given greater priority under Ms. Clarke, a liberal civil rights lawyer. The department is currently examining reports of abuse and neglect at prisons in Georgia and five detention facilities for juveniles in Texas.

Gov. Tate Reeves of Mississippi acknowledged the system’s shortcomings on Wednesday. Mr. Reeves, a Republican, declined to comment on the report’s conclusions, citing the possibility of a federal lawsuit against the state, but said he had helped push through incremental but important changes that demonstrated his commitment to improving conditions.

“We have made significant strides at Parchman in the last two years, everything from significantly reducing the number of inmates at Parchman, all the way to working with the legislature this year to get funding to increase the number of officers that we have,” he told reporters.

But he suggested that Washington needed to be patient with Mississippi, one of the poorest states in the country. “We know that personnel is an issue that we need to continue to improve,” he said, adding that the state intended to “do everything in our power to very quickly solve those challenges.”

But the Justice Department’s investigation said that lack of resources was not the only issue. Poor management of the complex, stemming from “nonfunctional accountability or quality assurance measures,” also contributed to the violent and squalid living conditions many inmates experienced.

Moreover, state officials for years displayed “deliberate indifference” to those conditions, contributing to an outbreak of violence at the prison that began on Dec. 31, 2019, and continued for weeks, the department reported.

“There had been widespread reports about unlivable and unsanitary conditions throughout Parchman; violent murders and suicides on the rise; staffing plummeting to dangerous levels; and mounting concerns that gangs were filling the void,” the report said.