According to the lawsuit, the beating happened at Men's Central Jail in February 2009.
The two deputies named in the lawsuit have already been charged criminally in a federal case and both have pleaded not guilty.
This lawsuit seeks unspecified monetary damages, claiming the sheriff's department did not protect a mentally ill inmate from being victimized.
Bret Phillips says he endured a vicious beating at the hands of deputies inside the jail. At a news conference announcing his lawsuit against the department, the 43-year-old didn't say a word. Instead, attorney Gloria Allred spoke on behalf of her client, who she says suffers from schizophrenia.
Allred says Phillips was handcuffed when he was knocked unconscious by two deputies. She said the beating was witnessed by civilian chaplain Paulino Juarez who was visiting the jail.
"He, to Father Paulino's knowledge and to his observation, did nothing to justify his having been beaten, did not resist, did not present any risk of harm," said Allred.
The two deputies accused of abusing Phillips both plead not guilty to federal charges in March. Joey Aguiar and Mariano Ramirez remain free on bonds of $25,000 each.
The chaplain mentioned in the federal indictment was interviewed by the ACLU, and says he saw Phillips lying in a pool of blood.
"He just was saying 'Stop, please stop, stop, I did nothing wrong," Juarez said.
The sheriff's department has for years endured allegations of inmate abuse. A federal investigation resulted in the indictments of 18 current and former deputy sheriffs in December. In January, longtime Sheriff Lee Baca resigned.
In regards to Wednesday's lawsuit, the department issued a statement: "The Sheriff's Department has not had the opportunity to review this lawsuit and will be unable to comment on pending litigation, however we take all allegations of inmate abuse very seriously and investigate every allegation."
Initially a sheriff's department investigation found that both deputies acted within policy, because, they say, Phillips tried to kick and spit at them. But the federal indictment contradicts those findings.
The lawsuit filed Wednesday seeks unspecified damages. Normally, the statute of limitations on a civil suit like this would have expired after two years, but Allred says that because of her client's mental illness, the statute of limitations does not apply.