The study by a panel of attorneys working for the Citizens Commission on Jail Violence was released Friday. It suggested that deputies used a "force first" approach with inmates, instead of using force as a last resort, even when no threat was present.
It also found Baca was largely insulated by his command staff from the problem due to a "code of silence."
Sheriff's Department spokesman Steve Whitmore says Baca strongly disagrees with many of the findings.
"Are there challenges in our jails? Absolutely. Has he acknowledged that? Yes," Whitmore said.
The department is expected to soon issue a report of its separate investigation of the jails. Whitmore said "people are going to be somewhat surprised" by the findings in the review ordered by Baca, but he did not elaborate.
The Associated Press contributed to this report.