A new crisis is roiling the scandal-plagued city Correction Department, the Voice has learned: A female inmate says she was sexually assaulted by at least one other woman in her cell in the Rikers Island jail.

A reported sexual assault in the women’s jail is extremely unusual, and this allegation has been handled with great secrecy by the department.

The alleged victim, whose identity is being withheld by the Voice, claims that someone entered her cell in the 1,000-bed Rose M. Singer Center while she was asleep, sometime before 6 a.m. on July 3. She says the intruder (or intruders) bound and gagged her with bedsheets and then used a dildo-like object to sexually assault her. Other inmates may have acted as lookouts during the alleged assault.

The woman, who was being held on grand-larceny charges for the past three months, was discovered at about 6 a.m. by a guard and a captain who were touring the building. There’s no doubt that she had been trussed up: The guard saw her lying on her back on the floor of her cell with bedsheets wrapped around her neck, mouth, and legs. She had also been blindfolded. The incident was reported to central command at 7:30 a.m., and the woman was transported to the Elmhurst Hospital Center.

Because she didn’t share a cell with anyone, a major question is how the alleged assault happened in the first place. Officials won’t talk about the investigation, and there’s no word on whether any arrests have been made.

The officials at 60 Hudson Street who run Rikers have had their hands full over the past couple of months with incidents that have become public. And it’s not just the scandal over those guards who allegedly passed accused cop killer Lee Woods pot, cigarettes, and alcohol.

More seriously, there was the April 27 suicide of 18-year-old Steven Morales in the high-security close-custody unit, and new questions about the death last year of mentally ill inmate Jermele Kelly in the Bellevue Hospital psychiatric ward following a violent encounter with correction officers. (Both stories were first reported in the Voice.)

In addition, there was the case of a guard who ordered young inmates to assault another inmate, and a bushel of guards who were busted for smuggling contraband to inmates. And just last week, inmate Nikholas Dadiani literally walked out of the jail, past three guards, and wasn’t picked up until he neared a bus stop that would have taken him to Queens Plaza.

According to one account of this new allegation of sexual assault, the incident took place during breakfast, when cells doors were open. Typically, breakfast is served to inmates from about 4:30 a.m. to about 6 a.m., but that time frame varies from jail to jail at Rikers.

Under Correction Department rules, inmates don’t have to leave their cells for breakfast, and many simply choose to continue sleeping. But the rules state that those inmates’ cell doors should be closed, specifically because of the danger of inmates entering a cell and assaulting fellow prisoners. That rule may have been bent, if not broken, here.

“Hypothetically, there would be enough time for such an assault even if the officer was doing everything he was supposed to be doing,” a department source says. “If the cells are left open, the officer is supervising the meal, and the inmate is gagged, it could happen.”

Another possibility is that the intruder entered the woman’s cell before the breakfast period, while she was sleeping. That would have meant that a guard would’ve had to open the cell door for an assault to occur.

And what about a motive? One source suggests that the woman was targeted in a power play by another inmate anxious to flex her muscles.

At any rate, authorities aren’t confirming either scenario—or a third possibility: that the claim is false.

Correction Department spokesman Stephen Morello declined to comment on the investigation but said: “We do not tolerate any type of sexual abuse by anyone in the jails. For more than five years, we have engaged in a campaign to prevent it .”

The Bronx District Attorney’s Office declined to comment.