The report did not contain highly publicised incidents in late 2006 at Jena, a small town in Louisiana, which involved hanging nooses reminiscent of those used in the lynching of black people in an earlier time and beatings of white students by black youngsters in retaliation.
Only 12,600 of the nation's more than 17,000 local, county, state and federal police agencies participated in the hate crime reporting programme in 2006, and neither Jena nor LaSalle Parish, the county where the town is, were among the agencies reporting.
Reverend Al Sharpton, a civil rights leader, said: "The FBI report confirms what we have been saying for many months about the severe increase in hate crimes.
"What is not reported, however, is the lack of prosecution and serious investigation by the justice department to counter this increase in hate crimes."
The two most frequent hate crimes in 2006 were property damage or vandalism, 2,911 offences, and intimidation, 2,046 offences. There were 860 aggravated assaults and 1,447 simple assaults, three murders, six rapes and 41 incidents of arson. Other offences included robbery, burglary, larceny, and motor vehicle theft.
As has been the case since the FBI began collecting hate crime data in 1991, the most frequent motivation was racial bias, accounting for 51.8 per cent of the incidents in 2006. That was down slightly from the 54.7 per cent in 2005.
Religious prejudice was blamed for 18.9 per cent of the incidents in 2006. The FBI said there were 967 attacks against Jewish targets and 156 anti-Muslim incidents.
Lack of full participation by the more than 17,000 police agencies around the nation somewhat undermines year-to-year comparisons.
Al Jazeera is not responsible for the content of external websites.