Friday's indictment was the latest in a series of events that began last month when a federal judge rejected a plea agreement limiting Baca's prison time to six months on the single false statement charge.
U.S. District Judge Percy Anderson said that was too lenient for the man who led the Sheriff's Department during a period when deputies covered up for one another and violently attacked inmates.
Last Monday, Baca failed to reach a new settlement with prosecutors and withdrew his guilty plea rather than let Anderson sentence him to up to five years, setting the stage for the new charges and a high-stakes trial.
In Friday's indictment, prosecutors accuse Baca of "creating an environment" in which his subordinates viewed the FBI as an adversary and of tasking his second-in-command, Paul Tanaka, with carrying out the scheme to obstruct the federal investigation into brutality and corruption by jail deputies.
Michael Zweiback, one of Baca's attorneys, called the indictment "weak" and said prosecutors were punishing his client for going to trial.