Starting next week, newly convicted, low-level felons who used to be sent to state prison will be sent to county jails. Those who go to jail in Los Angeles will find a system under siege.

This week, Sheriff Lee Baca publicly denounced an FBI investigation into his agency, after an LA Times story revealed federal agents paid a deputy $1,500 to smuggle a cell phone into the men's central jail.

Baca called the operation "illegal" and "unacceptable."

Over the years, there have been a number of allegations of police brutality, but it's usually the inmate's word against a deputy's. Most of the time, there isn't an outside witness. Now the American Civil Liberties Union of Southern California has delivered three. The California Report's LA Bureau Chief Krissy Clark has more.

Krissy Clark: L.A. is the state's largest jail system and for decades, it's been under scrutiny for a pattern of abuses by deputies. A federal civil rights law suit 35 years ago lead to court appointed monitoring by the American Civil Liberties Union. The group's latest report to the court finds incidents of jailers brutalizing inmates at epidemic levels.

Paulino Juarez: I hear somebody screaming.

Clark: Paulino Juarez is a chaplain. In this ACLU video, he described what he saw while volunteering at a downtown jail.

Juarez:...And I see these three deputies beating this person, and... [crying] ...they were punching him. I saw the body lying down on the floor, I was shaking.

Clark: Every year, the ACLU documents dozens of allegations of abuse at L.A. county jails. What gives this year's report new force is that the claims don't just come from inmates -- but also from civilian witnesses -- including a volunteer writing tutor, and two chaplains.

Retired FBI official Tom Parker helped the ACLU prepare the report. During his career, he's overseen investigations of the Rodney King Beating and other police corruption charges, but he says those abuses pale in comparison.

Tom Parker: The evidence I've seen in my investigation, as a lifelong criminal justice professional, is absolutely overwhelming. It's systemic violence; it's misfeasance and malfeasance to the highest degree, and there is a prevalent and long term pattern of this going on.

Clark: Parker, and the ACLU are calling for the resignation of L.A.'s Sheriff Lee Baca.

Parker: Sherriff Lee Baca and his top management have totally abdicated their responsibilities to provide a safe, secure and corruption-free incarceration environment.

Clark: The Sheriff's office said Baca was unavailable to respond for this story. In an interview on Fox 11 news this week, he defended his ability to manage L.A.'s severely crowded jails.

Sheriff Lee Baca: And let's make one thing clear: inmates attack deputies; deputies can't just let that happen. They will use responsive force. And the whole idea of how this all happens, is investigated thoroughly.

Clark: The sheriff says the county has its own office of independent review, and all allegations of deputy abuse get a second look from Michael Gennaco.

Michael Gennaco: My responsibility is when every case comes in, to make sure it gets a thorough investigation, and if it proves a violation of misconduct or policy violations, the deputies are held accountable.

Clark: Gennaco says, claims of deputy abuse from inmates, and even eyewitnesses, often don't hold up. In fact, he says, they looked into Chaplin Paulino Juarez' claims.

Gennaco: The interview with inmates shortly after the incident, captured on video, did not match up with what the chaplain believed he saw, with regard to the force, the extent of the beating.

Clark: But ACLU lawyers are critical of the whole process for how these complaints are investigated. They say, routinely, accused deputies are in the room when an inmate is interviewed about what happened.

They point to the case of Gordon Grbavac. He spent a week in an LA jail on charges that were ultimately dropped. The floor he was on is notorious for having abusive deputies. While he was there, he says two deputies, unprovoked, slammed his head into a glass wall several times.

Gordon Grbavac: There was blood all over the floor, and then the supervisor had come and asked what happened. I told them that these two sheriffs' deputies assaulted me.

He said he'd be right back, when he left to get the video camera, one of the white sheriff's deputies told me to change my story or, 'we're going to teach you what we do to people like you around here.'

Clark: The ACLU plans to file a civil rights case against the sheriffs department soon. The FBI is also probing claims of deputy abuse at the LA county jail.