The department's inspector general, Richard Skinner, says at least 15 of the guns lost in bowling alleys, public restrooms, unlocked cars and other unsecure areas ended up in the hands of felons, USA Today reported Thursday.
Skinner documented 289 incidents of missing firearms from fiscal 2006 through 2008.
Not all were lost because of negligence, his report says. Some disappeared in the aftermath of Hurricane Katrina and others were stolen from safes.
Homeland Security says employees who lost firearms have been fired or suspended.
The report does not say if any of the lost firearms were used in crimes.
A spokesperson for Homeland Security says workers are getting extra training and officials are improving tracking and inspection of guns.