Men's Central Jail

An inmates flashes a hand signal at the Men's Central Jail in downtown Los Angeles. Two Los Angeles County sheriff's deputies were indicted on charges of assaulting an inmate and submitting false reports. (Reed Saxon / Associated Press / December 9, 2013)

Federal prosecutors announced charges Friday against two Los Angeles County sheriff's deputies accused of assaulting a handcuffed inmate in a case that broadens the FBI's ongoing inquiry and raises new questions about how the Sheriff's Department has investigated deputy misconduct in the nation's largest jail system.

Sheriff's officials previously rejected allegations that the deputies used excessive force despite a jail chaplain coming forward to say that he witnessed the 2009 incident and believed the deputies beat a helpless inmate. The sheriff's watchdog reviewed the case but signed off on the department's findings.

A second inquiry by a special task force launched in 2011 to review accusations of brutality in the jails submitted its investigation to the district attorney's office nearly a year after the legal deadline for filing criminal charges in state court, according to a district attorney's memo obtained by The Times. The deputies were not disciplined by the department in connection with the incident, a sheriff's spokesman said.

FEDERAL INDICTMENT: Prosecutors' allegations

Including the new charges, 21 current and former sheriff's officials have been accused of crimes in the FBI's three-year investigation into brutality and other misconduct in the department.

Miriam Krinsky, executive director of a county commission that was created in response to the jail abuse scandal, said the indictment provides more evidence that the Sheriff's Department failed for years to hold its deputies accountable for misconduct.

"It's simply another example of the need to be terribly concerned about what checks and balances are in place within the department," she said.

Interim Sheriff John Scott said in a statement that the department was cooperating with federal authorities and that his "No. 1 priority is to ensure that the department continues the substantial progress it has made in reforming and improving our jail system and culture."

He said the indictment underscores "that everyone in this department should and will be held accountable for their actions. Abuse of authority will not be tolerated."

Federal authorities allege that Deputies Joey Aguiar, 26, and Mariano Ramirez, 38, violated the civil rights of the inmate by assaulting him Feb. 11, 2009, in the Men's Central Jail. The deputies could not be reached for comment.

Prosecutors contend that the man was handcuffed to a waist chain during the attack. The indictment accuses the deputies of kicking the inmate in the head and upper body, striking him with a flashlight and pepper-spraying him in the face.

The indictment identifies the inmate as BP, but the district attorney's memo identifies him as Brett Phillips.

COURT DECLARATION: Jailhouse chaplain describes alleged inmate beating

The memo, written by Deputy Dist. Atty. Fernando Guzman, provides additional details about the incident, saying that four sheriff's deputies wrote reports explaining that the force was used after Phillips tried to assault Aguiar. Aguiar and Ramirez, the memo says, punched Phillips five to eight times in the rib area while Ramirez struck the inmate two to three times in the leg and elbow with a flashlight.

Sgt. Ernie Barbosa corroborated the deputies' account by saying that he saw the inmate try to kick the deputies, according to the memo, which identified the other deputies involved in the force as Mario Pinedo and Rene Madrid. (The federal indictment states that the grand jury knows of other people involved in the incident but does not identify anyone other than Aguiar and Ramirez.)

Medical records from the jail show that Phillips suffered two raised bruises on his forehead, including one with a cut, but no fractures. A nurse noted scrapes to both of the inmate's wrists and his left eyebrow, according to the memo.

Federal prosecutors say Aguiar and Ramirez submitted reports that falsely claimed the inmate tried to head-butt Aguiar and kick at deputies. The indictment says the Sheriff's Department used the reports to begin the process of referring the inmate to the district attorney's office for criminal prosecution. The office rejected filing charges, according to several sources.

A chaplain said he came forward a day after the incident to say that he was a witness. In a report that he gave to the department days later, Deacon Paulino Juarez wrote that he watched in horror as deputies beat the inmate bloody as the victim shouted, "Please stop!" He said the deputies kicked and stomped on the inmate.

"I felt that I had witnessed a crime," he wrote.

Nevertheless, the department concluded that the force was within policy.