By Paula Lehman

LOS ANGELES (Reuters) - Former Los Angeles County Sheriff Lee Baca pleaded not guilty on Friday to charges he sought to obstruct a federal corruption probe that overshadowed the final years of his tenure as chief custodian of the nation's largest county jail system.

Baca, who is 74 and suffers from Alzheimer's disease, was indicted last week on three new criminal charges after he backed out of an earlier plea agreement rather than face a sentence tougher than the six-month term a federal judge rejected as too lenient.

He entered a not guilty plea on Friday to all three new felony charges - obstruction of justice, conspiracy to obstruct justice and lying to federal investigators. He could face up to 20 years in prison if convicted.

Questioned by U.S. District Judge Percy Anderson before entering his plea on whether he felt competent to do so, Baca replied, "My mind is clear enough, but there are circumstances where I have cloudiness in my brain, and I've had that for quite awhile."

When Anderson asked Baca if his state of mind prevented him from understanding the charges against him, the former sheriff answered, "Not at this moment."

Federal prosecutors previously had agreed to recommend a prison term of no more than six months in return for Baca's guilty plea to a single count of making a false statement to investigators.

Both prosecutors and defense lawyers at the time cited the retired lawman's then-recent Alzheimer's diagnosis in their reasoning under the original deal for seeking a sentence that was far less than the maximum five-year penalty.

But in a surprise decision in July, Anderson refused to approve that agreement, ruling that it understated the seriousness of the offense.

Baca served as the top elected law enforcement official in Los Angeles for 15 years before retiring in January 2014 amid a federal investigation of inmate abuse and other wrongdoing, including cover-up attempts, at two downtown lockups.

The overall jail system his department runs houses some 18,000 inmates. Seventeen other officials have been convicted of criminal charges in the misconduct probe, including Baca's former second-in-command, who was sentenced to five years in prison.

Baca pleaded guilty in February to making false statements when he asserted in a 2013 interview by federal investigators that he had no prior knowledge of his deputies' efforts to harass an FBI agent involved in the jail corruption probe.

Specifically, Baca admitted he actually was aware that his deputies planned to intimidate the agent and that he had directed them to "do everything but put handcuffs" on her.

His lawyer, Nathan Hochman, told reporters on Friday that nothing Baca said as part of his now-withdrawn guilty plea could be used against him at trial. Hochman also said the defense would seek a medical examination of Baca to better determine "the state of his competency."

On Friday, Baca appeared confused at times, seeming unsure whether to stand or be seated at the start of the proceedings, and about how to answer some of the questions put to him by the judge.

(This version of the story corrects the name of the defense lawyer to Nathan Hochman, from Michael Zweiback, in paragraph 13)

(Reporting by Paula Lehman in Los Angeles; Writing and additional reporting by Steve Gorman; Editing by Tom Brown and Leslie Adler)