The Federal Bureau of Investigation's crime report for 2005 showed that violent crime as a whole - including robbery, murder and assault - rose by 2.5% across the country.
Murder rates were particularly high in America's medium-sized cities with populations between 50,000 and 500,000, where increases of 9.4% to 12.5% were recorded.
US Midwestern states registered the worst of all regions, with a 5.7% increase in reported violent crime.
However, recorded rapes decreased overall by 1.9% and overall rates of some violent crimes in the country's largest cities decreased slightly.
US Justice Department officials said the statistics showed that while major cities were trying to tackle crime rates, smaller ones needed firmer policies.
"We need to find out what's going on in the smaller cities, how we can partner with them where it's needed and how can we best apply those best practices to the smaller cities," said Regina Schofield, an official with the Department's bureau of statistics.
Attorney General Alberto Gonzales has reportedly directed Justice Department and FBI experts to look at the crime data and report back on what could be the cause of the increase, officials said.
Richard Hertling, principal deputy assistant attorney general, said that while the numbers were "something to watch", they did not necessarily reflect a trend.
However, some criminologists said they were concerned by the figures and criticised the government for slashing domestic crimefighting budgets and focusing police efforts on combating terrorism.
"Hopefully in Washington it will be seen as a wake-up call to get back to the task of fighting crime the way we're fighting terrorism"
James Fox, criminologist
"Hopefully in Washington [the report] will be seen as a wake up call to get back to the task of fighting crime the way we're fighting terrorism," criminologist James Fox at Northeastern University said on Tuesday.
"We're now slashing budgets for police, we're slashing crime prevention programs for kids and we no longer seem to have rational policies with regard to guns," he added.