LOS ANGELES » The case of the vanishing inmate at the Los Angeles County jail nearly went all the way to the top.

The former second-in-command of the nation’s largest sheriff’s department and a high-ranking official who was supposed to investigate crimes by deputies surrendered Thursday on charges they hid an FBI jailhouse informant to hinder a federal investigation into abuse by guards.

"The scheme to obstruct justice rose to the executive level of the Sheriff’s Department," Acting U.S. Attorney Stephanie Yonekura said at a news conference. "Both men were aware that there was rampant abuse at the jail, and both men were aware that the internal investigations of that abuse were insufficient."

Former Undersheriff Paul Tanaka and former Capt. William Thomas Carey pleaded not guilty in U.S. District Court to charges of conspiracy and obstruction of justice.

The men, both 56, are the highest-ranking officials charged in the long-running investigation of jailhouse corruption and abuse that tarnished the career of Sheriff Lee Baca, who resigned last year.

Federal prosecutors wouldn’t comment on whether Baca played a role in the cover-up or whether he would face charges.

The indictment stems from an investigation of civil rights abuses that blossomed into an obstruction-of-justice case when deputies and higher-ups discovered in the summer of 2011 that an inmate found with a cellphone was providing information to the FBI about beatings by deputies. The phone was smuggled to the inmate by a corrupt deputy.

Tanaka and Carey were involved from the get-go in taking extraordinary steps to thwart the investigation, Yonekura said.

The FBI wanted the informant to testify to a grand jury, but agents couldn’t find him.

Two lieutenants, two sergeants and three deputies were convicted of participating in the cover-up that involved shuttling the informant, Anthony Brown, between different jails under different names. The two sergeants tried to intimidate the lead FBI agent by threatening her with arrest.

The defense argued that the employees were following orders from higher-ups.

Tanaka testified for his underlings that Brown was being relocated to protect him because he was a snitch and so the department could conduct its own investigation into the smuggled phone.

Tanaka’s testimony will probably be used against him at his own trial, Yonekura said.

Defense lawyer H. Dean Steward said Tanaka plans to aggressively defend himself in court.

Carey was charged with two counts of perjury for lying at the trials of his subordinates about why Brown was moved, the indictment said. Carey’s lawyer declined to comment.

With the new indictment, a total of 23 members of the department have been charged with crimes ranging from civil rights violations to gun charges and obstruction of justice. Three deputies, all brothers, were acquitted of a mortgage fraud scheme.

The indictment alleged Tanaka helped foster a culture of abuse by minimizing investigations into misconduct and encouraging supervisors to let deputies operate in a "gray area" between justifiable conduct and abuse.

"We all know there is gray in life, but when it comes to the law, there’s black and there’s white," said David Bowdich, assistant director of the FBI’s Los Angeles office. "There’s no area for gray where he was looking for it."

Despite being aware of concerns from outside the department about a lack of investigations into abuse, Tanaka advocated chopping the Internal Affairs Bureau from 45 investigators to one, authorities said.

Tanaka retired from the sheriff’s department in 2013 and serves as mayor of the nearby city of Gardena. He ran to replace Baca as sheriff but lost by a wide margin to Jim McDonnell, who has vowed to reform the troubled agency.

Shortly after McDonnell took office last year, the department agreed to federal court oversight and new use-of-force policies to settle a class-action lawsuit brought by inmates who said they were beaten by guards.

Nine deputies still face charges of violating the civil rights of inmates and jail visitors, including an Austrian consulate official who was handcuffed and detained with her husband.

Yonekura said her office will continue investigating civil rights abuses by the department, but she’ll never know what they might have uncovered if their investigation wasn’t impeded.