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 number of hate crimes in 2016 was 6,121 - about a 5% jump from 2015.
Minnesota reported 119 hate crimes past year, up from 109 in 2015. These agencies provided from one to 12 months' worth of data about bias-motivated crime, and of those agencies, 1,776 reported one or more incidents.
Six hate crimes were related to religion, while five were associated with sexual orientation.
The latest statistics are based on voluntary reporting from almost 16,000 U.S. law enforcement agencies.
On Monday, Sessions said the Justice Department is awaiting a full report from a task force on steps it can take to improve training for prosecutors and investigators, boost data collection on hate crimes and partner with local officials and communities.
Attorney General Jeff Sessions said the Justice Department is now engaging with state and local leaders and to find ways to better prevent and prosecute hate crimes. Hate incidents increased from 203 in 2015 to 285 in 2016. Some agencies also may not determine an incident is a hate crime until after the FBI's deadline to report.
Crimes motivated by a religious bias were the second-most reported type of hate crime.
"No person should have to fear being violently attacked because of who they are, what they believe or how they worship", he said. But incidents motivated by anti-Muslim bias saw the greatest increase out of religion-motivated crimes.
Maryland State Police report not just hate "crimes", but also "incidents", which could include things such as intimidation, which may not be considered a crime.
Dozens of cities with more than 100,000 residents either reported zero hate crimes or did not submit their hate crime data, according toananalysis by the Anti-Defamation League, a civil rights organization, which has called for better reporting.