New Jersey’s attorney general has ordered an overhaul of the internal affairs unit of the State Police and seized control of its human resources department after concluding that disciplinary investigations had been “weaponized” against some troopers.

The attorney general, Matthew J. Platkin, announced the restructuring on Tuesday as he released two scathing reports that detailed bias in the agency’s promotional policies and systemic flaws in its ability to police itself.

The reports, including a four-year, taxpayer-funded review by an outside law firm that conducted interviews with 150 troopers, offered an ugly glimpse into how New Jersey’s largest policing agency handled reports of racism and allegations of sexual misconduct.

“These investigations revealed deeply troubling conduct and systemic problems within the New Jersey State Police that demand reform,” Mr. Platkin said in a statement.

“There are favored members at the State Police, and some members hesitate to report discrimination or misconduct for fear of reprisals,” he added.

His office recommended more than two dozen policy changes, including disclosure of complaints made against senior State Police officers and alterations to its sick-leave policies and physical fitness tests that most often penalize women. He also ordered the agency to restructure its academy training program.