Reports of sexual assault by US military personnel against both fellow troops and civilians rose by some 8% last year to 2,923, the Pentagon says.
The number of incidents reported in Iraq and Afghanistan rose by about a quarter on the previous year to 163.
Pentagon officials say the jump in reports suggests the department's policy of encouraging victims to come forward is bearing results.
But they estimate that no more than 20% of attacks are actually reported.
"Given the fear and stigma associated with the crime, sexual assault remains one of our nation's most under-reported crimes in both the military and civilian community," said Dr Kaye Whitley, the director of the Pentagon's Sexual Assault and Prevention Office.
She said the rise in reported incidents did not necessarily mean sex crimes were increasing but that victims were less afraid to come forward.
"The department has been aggressively pursuing efforts to increase reporting and convince more victims to seek care and support services," she said.
Among the report's findings:
There were 2,923 reported sexual assaults in the 2008 fiscal year, up from 2,688 in 2007
There 251 incidents in combat areas, including 141 in Iraq and 22 in Afghanistan
Investigations took place in 2,763 cases. In 832 cases, action was taken, including 317 courts-martial, a rise of 38%
Of the 6.8% of women and 1.8% of men who indicated they had experienced unwanted sexual contact, the majority - 79% of women and 78% of men - chose not to report it.
The Pentagon acknowledges that despite the increase in reported attacks and action taken, "the question will be asked why every single reported case did not go to courts-martial".
One possible explanation, the report says, is the complexity of sexual assault investigations and prosecutions.
Unwanted sexual contact is defined as ranging from touching to rape. Of the reported attacks, 63% were rape or aggravated assault.
The report covers rape and sexual assaults across the 1.4 million active members of the US military.
Cases are defined as involving at least one member of the military as either alleged attacker or victim.
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