Officers James Nichols, 44, and Luis Valenzuela, 43, are charged with multiple counts of sexual assault, including rape under color of authority, according to a criminal complaint filed in Los Angeles Superior Court.
The alleged assaults in some cases took place while the officers were on duty, according to prosecutors, including in their police car. Valenzuela is accused of pointing a gun at one of the victims.
"These two officers have disgraced themselves. They've disgraced this badge. They've disgraced this office," Los Angeles Police Department Chief Charlie Beck said at a news conference.
The officers pleaded not guilty Thursday.
Each of the women had at one point been arrested by the officers during "narcotics-related" investigations, according to prosecutors.
The alleged assaults occurred between December 2008, when the officers first became partners, and March 2011. The alleged victims were ages 19, 24, 25 and 34 at the time.
The filing of criminal charges against officers for on-duty felony conduct is rare and represents a black eye for the LAPD.
Beck noted that his department conducted the criminal investigation of the officers and that detectives were continuing to work with prosecutors on the case against them.
"Any officer that abuses the public's trust is not welcome in the LAPD," Beck said earlier in a prepared statement.
In January, an Oklahoma City police officer was sentenced to 263 years in prison
after being convicted of raping multiple women he encountered as an officer. Prosecutors said Daniel Holtzclaw preyed on African-American women with drug or prostitution arrests because he assumed their criminal histories would undermine their credibility if they accused him.
The criminal charges against the Los Angeles officers come more than two years after a woman filed civil lawsuit against the officers alleging that they threatened to throw her in jail if she didn't have sex with them.
The case settled in January 2014 for $575,000, said the woman's attorney, Dennis Chang.
Chang said he was representing his client on a criminal drug charge when Valenzuela approached him and said he would help with her case if she'd agree to work as informant.
"It started like that," the lawyer said. "Then he started showing up drunk at her apartment at 3 a.m. saying: 'You haven't done enough for me. I can put you back in jail.' "
Another woman filed a similar suit in 2014. She said the officers befriended her and bought her food and alcohol. Then, they forced her into sex, according to the lawsuit filed in Los Angeles federal court.
She described an encounter in which she was walking her dog and the officers drove by in an unmarked car. They ordered her to get in, the lawsuit sates. They drove her to secluded location and Valenzuela sexually assaulted her in the back seat while Nichols held onto her dog and kept watch, the lawsuit alleges.
Afterward they threatened her not to report the assault, the lawsuit alleges.
"You don't want to go to jail, do you?" her complaint quotes the officers as saying.
Dan Miller, the woman's attorney, said the case recently settled, pending city council approval. He declined further comment.
CNN did not name the women in the lawsuits because they are alleged victims of sexual assault.
Attorney Robert Rico, who represents Nichols in administrative charges of sexual misconduct filed by LAPD, said the officer has been relieved of duty without pay for two years.
Rico said he did not know if the criminal charges mirror what's alleged in the administrative case. If they do, he said, "my client absolutely denies it."
Attorney Bill Seki represents Valenzuela, who faces similar internal charges at LAPD and has also been relieved of duty.
Seki said his client also denies the administrative charges. The lawyer, a former prosecutor in the District Attorney's office, said the criminal investigation of the officers had dragged on for years and that there were "issues of credibility" surrounding the victims.
Seki declined to elaborate.
Prosecutors said they will seek bail of $3.83 million for Nichols and $3.76 million for Valenzuela, according to a District Attorney's press release.