The trio of deputies face a host of felony and misdemeanor charges for orchestrating the brawls in what prosecutors described as a jailhouse "fight club."
In one case last year, a deputy allegedly ordered two inmates to fight one another and threatened to mace, shock or beat them
if they refused, authorities said.
The two inmates fought each other because they felt they had no choice, according to a press release by San Francisco County District Attorney George Gascon.
One of the inmates was substantially larger than the other and injured the smaller man's ribs in the forced bout, the release said.
Gascon described the alleged conduct of the deputies as "degrading and inhumane treatment" that "makes a mockery of our justice system."
"We, in conjunction with our law enforcement partners, will continue to seek out injustices such as these and hold those entrusted with upholding and enforcing the law to the highest standard," David J. Johnson, the FBI's top ranked agent in San Francisco said in joint statement with the Gascon.
The FBI assisted DA's investigators in the probe.
Prosecutors have obtained arrest warrants for Deputies Eugene A. Jones and Clifford T. Chiba and former Deputy Scott R. Neu, said Alex Bastian, according to the DA's office.
The three are charged in connection with the fights and other alleged abuses, including forcing inmates to exercise and to gamble for food, clean clothing and bedding. The fights are alleged to have occurred last year.
Neu and Jones are charged with felony assault under color of authority and face up to 10 years and five years imprisonment respectively if convicted. Chiba is charged with misdemeanor and cruel and unusual treatment of prisoners and faces up to 18 months if convicted.
Attorney Christopher J. Shea, who represents Chiba, declined comment on the charges, but was critical of Gascon for calling a press conference to announce them.
"It's political grandstanding at its worst," Shea said. "There's no reason to try to convict anyone in the court of public opinion. It's unprofessional."
Bastian said prosecutors are working with the defense attorneys to arrange dates and times for the deputies to surrender and appear in court. None of the current or former deputies were immediately available for comment.
Eileen Hirst, chief of staff for Sheriff Vicki Hennessy, who oversees the county jail system, welcomed news of the filings.
"We're very glad the investigation is finally over and this is in the hands of the courts," she said.