Rikers inmates reported 28 separate incidents of rape behind bars last year — but none of the incidents was shared with the NYPD, according to new court filings. View Full Caption Getty/ Spencer Platt

EAST ELMHURST — Rikers inmates reported 28 separate incidents of rape behind bars last year — but the NYPD wasn't told about any of them, according to new court filings.

The city's Department of Health and Mental Hygiene, which oversees health care at Rikers, alerted the Department of Correction of 116 total inmate allegations of sexual abuse in 2014 — 28 of which were allegations of rape — but the DOC only passed along two misdemeanor sex assaults to the NYPD, according to court documents filed by Public Advocate Letitia James.

In addition, 61 of the 116 sex abuse complaints were allegedly inflicted by jail staffers, court documents show.

“[Health department] data shows that DOC staff is alleged to have abused inmates at an alarming rate,” James wrote in court papers supporting a class action lawsuit that says city government has turned a blind eye to widespread sexual violence at the jail.

“Our affidavit proves the disturbing prevalence of sexual harassment and abuse allegations on Rikers Island, along with a stark lack of coordination between corrections and health care workers in the investigation of the incidents,” she added in a statement.

The DOC said it follows NYPD procedures in investigating and reporting sexual allegations.

“[DOC[ Commissioner Ponte has zero tolerance for any sexual harassment or violence against staff or inmates,” the DOC said in a statement.

But according to James's court papers, the DOC is substantiating sexual allegations “at startlingly low rates.”

Claims at Rikers are only substantiated about 2.5 percent of the time, according to the filing — almost five times less frequently than jails nationwide, according to federal data.

James also called out an “alarming discrepancy” between the number of reported incidents recorded by the Department of Correction and the reports made to the city’s health department, which oversees care at Rikers.

In 2013, the most recent year for which both agencies’ counts are available, DOC reported 29 fewer incidents than the Department of Health and Mental Hygiene.

“It is inexplicable why the data reported by DOC is much lower than data from DOHMH,” James wrote.

DOC said its count is lower because the department excludes complaints it says do not rise to the level mandated by federal law, such as those that took place during frisks.

And while the population at Rikers has gone down over the past three years, sex abuse allegations have not decreased, according to health department data. Transgender inmates accounted for nearly 30 percent of those reporting violations against them last year, stats show.

The statistics come amid widespread criticism of the Department of Correction's handling of Rikers inmates, including allegations by US Attorney Preet Bharara that it allowed guards to abuse teen inmates in an "unchecked cycle of violence."

James urged the Board of Correction, which oversees Rikers, to make new rules “to better protect inmates from sexual violence.”

“They must start tackling this problem with the urgency it deserves,” she said.