A Suffolk County police officer was arrested Thursday by the FBI on charges that he twice forced a woman in custody to engage in a sex act at a police precinct, authorities said.

Christopher McCoy, 38, of Sayville, was charged with violating the civil rights of the woman he arrested in March in Wyandanch after a traffic stop, according to court papers filed in U.S. District Court in Central Islip.

The alleged attacks occurred while McCoy was alone with the woman — identified only as Jane Doe — at the First Precinct in West Babylon, prosecutors said in the criminal complaint.

“Law enforcement officials are duty-bound to uphold the Constitution and protect all of our citizens, and certainly not to abuse them,” Eastern District U.S. Attorney Bridget Rohde said in a statement. “No dereliction of this duty will be tolerated.”

Suffolk Police Commissioner Timothy Sini said the department intends to fire the officer.

“Look, this is disgusting. This is rape,” said Sini, who spoke to reporters Thursday afternoon at police headquarters in Yaphank. “We’re not going to tolerate this, obviously.”

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As part of a thorough review of the department’s rules and procedures, Sini said livestreaming cameras have been installed in all First Precinct interview rooms, and the department plans in the “very near future” to put them in all precincts.

The live video can be viewed by the desk officer, desk sergeant and squad sergeant, Sini said, calling it “a significant deterrent for criminal misconduct.”

In a federal lawsuit filed in May, the woman, now 31, said she reported the alleged sex abuse to the FBI because she feared Suffolk police “would do nothing . . . or worse, retaliate against her.”

McCoy is charged with aggravated sexual abuse by one acting under color of law, because he forced the woman to have oral sex twice. He faces up to 20 years in prison, if convicted.

On March 16, McCoy took the woman into “an isolated room where the two were alone behind a closed door,” according to the complaint filed by Eastern District prosecutor Lara Treinis Gatz.

According to prosecutors, he pressed against her, unzipped his pants and attempted to get her to engage in a sexual act, but she refused. He ended up holding her down and forcing himself on her. That encounter ended when another person entered the room, the court papers said.

Later that day, McCoy and his partner took the woman into the same back room and the partner then left, the court papers said. The papers said McCoy again pushed himself on her and “said in sum and substance, ‘Let’s go, don’t make this hard.’ ”

McCoy, who did not enter a plea Thursday, was released on $500,000 bond and barred from contacting the woman, possessing firearms and leaving the state.

On April 6, FBI agents interviewed McCoy, who initially denied any sexual contact with the woman. When the agents advised McCoy that they were going to use an oral swab to collect DNA from his cheek, “he admitted having engaged in oral sex with Jane Doe,” according to the complaint.

An FBI forensic examiner subsequently compared a stain found on Jane Doe’s shirt to the swab and concluded McCoy “was a likely DNA contributor to the stain,” which was semen, according to the complaint.

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Brian T. Egan of Patchogue, one of Jane Doe’s civil attorneys, said “the victim declines to make any public statements outside of court.”

McCoy’s attorneys, William Petrillo and Edward Sapone of Garden City, said it would be “inappropriate to comment on the reliability of the complaint” or the suit that was “filed so quickly.”

McCoy was with the NYPD for about a year and a half before joining the Suffolk department about 10 years ago, the lawyers said.

The department first learned of the allegations against McCoy on April 5, Sini said. The following day, he was suspended without pay, and administrative charges were filed against him.

Sini said the department participated in the FBI’s probe and is “aggressively” investigating the allegations internally.

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The woman said in her suit that McCoy and a partner in a patrol car stopped a car in which she was a passenger. She said McCoy told her she had outstanding warrants for vehicle and traffic violations, but she said she told him she had court documents showing the warrants had been addressed.

She also alleges in the suit that McCoy later sent her harassing text messages. In the criminal complaint, prosecutors said the FBI traced the messages to McCoy’s phone.

William F. Sweeney Jr., assistant director-in-charge of the FBI’s New York field office, said the McCoy investigation is continuing and urged “any individuals who may have been a victim of McCoy to call us at 212-384-2166.”