The report, by the Defense Department's Sexual Assault Prevention and Response Office, details allegations by service branch for the fiscal years 2013-2016, with the Army -- the largest branch of the military -- reporting 8,294 cases in all.
The Navy meanwhile reported 4,788 cases, the Marine Corps 3,400 and the Air Force 8,876.
The military has about 1.3 million active-duty troops.
The publication of the report comes amid a sexual harassment scandal that has shaken America, with each new day bringing fresh allegations against powerful men from across the political, cultural and business landscape.
Since 2012, the Pentagon's annual reports have reported drops in the numbers of sexual assault among the force, officials said.
In 2016, data showed a decrease from 6.1 per cent of active duty women in 2012 to 4.3 per cent in 2016, and from 1.2 per cent of active duty men in 2012 to 0.6 per cent in 2016.
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