A top department official described the backlog as "massive."
The National Institute of Justice, a Justice Department office, reports that a mail-in survey of state and local crime labs found 542,700 unsolved cases with DNA evidence that has not been tested.
Most of the backlogged cases — 264,000 — involved non-violent crimes. But 221,000 were violent crimes, including roughly 52,000 homicides and 169,000 rapes.
The institute's report said the backlog represented a neglected crime-fighting tool.
"There are numerous crimes that are potentially preventable through better, more efficient use of forensic DNA analysis," the report found.
"A review of specific cases in nineteen states reveals over 100 serious crimes that could have been prevented through either the inclusion of all convicted felons in the database or shorter DNA analysis processing times," it said.
The survey found that about half of labs said the reason they had backlogged cases was that they had seen no reason to test the material, either because prosecutors said they didn't need DNA evidence or because no suspect had been identified in the case.
"To be sure, this is exactly the kind of situation where an offender DNA database would be most useful," the report read.
The study cited one example where the head of the sex assault unit in one state's largest law enforcement agency said the unit had never asked for testing on a DNA sample.
About a quarter of labs — 23.8 percent — said the backlog was due to staffing and funding constraints.
Analyzing biological evidence is time-consuming and costly — it takes labs between 29 and 30 weeks to process a rape kit, and each kit costs an average $1,100 to test.
And the federal government is doing relatively little to offset those costs — only one in five state labs, and about one in 20 local labs, received more than half of its funding from the federal government.
The report concluded that: "Clearly, not only is there a greater potential role for the federal government to play in assisting with the current backlog problem, but there is also a certain need for state and local governments to re-evaluate their degree of investment," in DNA testing.
The Justice Department has proposed a $1 billion program to improve DNA testing around the country, said Deborah Daniels, assistant attorney general for the Office Of Justice Programs. She described the backlog as "massive."
"Forensic DNA evidence has tremendous potential to solve some of our nation's most serious crimes, but this study shows DNA is not currently being used to its full potential," said Daniels in a statement.
Daniels said that DNA analysis "clearly demonstrates the potential to prevent repeat offender criminals from victimizing multiple citizens."