The Anti-Defamation League noted that almost 90 cities with more than 100,000 residents either reported no hate crimes in 2016 or did not provide any data to the Federal Bureau of Investigation.
The report - which is based on 2016 data voluntarily submitted by about 15,000 law agencies - shows a five percent increase in hate crimes from 2015 and a 10 percent increase from 2014, Reuters reports.
Furthermore, there were another 7,321 related offenses stemming from bias against race, religion, sexual orientation, and other traits.
1,218 hate crimes were based on bias against certain sexual orientations.
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Religious bias motivated 1,538 hate crimes previous year - over half against Jews, and about one-quarter against Muslims.More news: Portia de Rossi makes sexual harassment claims against Steven Seagal
Hate crimes happened in a variety of locations.
Although the Department of Justice estimates that 250,000 hate crimes are committed per year, the majority of those crimes go unreported.
In April, the Anti-Defamation League reported 1,266 anti-Semitic incidents in 2016, a 35 percent increase from 2015.
The Southern Poverty Law Center, a non-profit which tracks hate groups, attributed the bump to the 2016 presidential election, in which Donald Trump assailed Muslims and Hispanics as extremists and illegal immigrants. Black people were the targets of hate crimes in half of all racial cases, while white people were the targets about 20 percent of the time. However, no link has been proven between the election and the increase.
However, anti-white and anti-Hispanic race-motivated crimes both increased in 2016. "Earlier this year we've seen the targeting of mosques and Sikh temples, we've seen black churches burned across the country so it all leads to the performance where people are acting out the physical violence against people who are different or not like them".
The FBI's hate crime statistics lag by about a year and widely believed to underreport the extent of hate crimes in America.