Eyewitness News examined the same data and found the issue is one of how sex crimes get classified.
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Take 2017, the latest year with available FBI statistics.
Using data provided by New York City, the FBI counts 2,375 incidents of rape but the NYPD looks at that same data and counts just 1,449, roughly 38% fewer rapes.
The discrepancy results from a difference in how both agencies classify crimes.
The FBI uses an expanded definition of rape to include multiple kinds of penetration including forced oral and anal sex.
The NYPD uses a much more specific definition of rape outlined in the New York State penal code.
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As a result, when the NYPD releases weekly and monthly crime statistics in its Compstat reports, many serious sex crimes get excluded from the rape category of that report.
Only incidents that fall under New York state's definition of rape are independently reported, a footnote warns readers about the discrepancy.
Other still serious sex crimes are reported separately, in detail, quarterly and annually by the Special Victims Unit.
"It's only New York City that is designating rape as a narrow set of offenses that actually use that word," said Council Member Rory Lancman, who called NYPD's reporting misleading. "I shouldn't have to find a footnote, interpret a footnote and then find out how many rapes are actually happening," he said.
Thursday, Deputy Chief Judith Harrison, the commanding officer over SVU, acknowledged she understands why the public might misinterpret the data NYPD provides but she added it was never the NYPD's intent to be misleading.
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"We do report these crimes to the public," Harrison said. "We do report rapes in a way consistent with the NYPD penal code but we also subscribe to the FBI uniform crime reporting mandate."
In response to the confusion, Harrison added that the NYPD is working on a more inclusive definition of rape, similar to the FBI's expanded definition of rape, to guide its regular compstat crime statistics reports so that the report more closely reflects the public's view of rapes.
"We have an obligation to inform the public," Harrison said. "If there is a way we can improve to better inform the public we are committed to that."
Harrison added that whether or not a sex crime is classified as a rape by the department, all crimes reported to SVU are taken seriously.
"We investigate every crime regardless of classification," Harrison said. "We don't think one crime is less than another."
Victims of rape can call the NYPD rape hotline 24/7. That number is 212-267-RAPE (7273).
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