The 5.3 percent drop in violent crime was accompanied by a 4.6 percent drop in property crime, marking the seventh consecutive year that nonviolent crime has dropped.
Each of the violent crime categories decreased from 2008, as did each of the property crime categories.
Murder fell by 7.3 percent, robbery by 8 percent, aggravated assault by 4.2 percent and rape by 2.6 percent.
Motor vehicle theft was down by 17.1 percent, larceny by 4 percent and burglary by 1.3 percent.
The bureau said victims of property crime, aside from arson, lost an estimated $15.2 billion during 2009.
Data for the FBI's annual crime report comes from 17,985 governmental units and universities and colleges representing over 96 percent of the nation's population.
James Alan Fox, a criminologist at Northeastern University, said that while the downward trend is encouraging, the economy "could come back to haunt us" because of a nearly 10 percent drop per capita in police budgets in the past few years.
"There is a connection between the economy and crime rates, but it's not that when the economy is bad, people go out and commit crime," said Fox. "When the economy is bad, there are budget cuts. Less is spent on youth crime prevention and crime control on the street."