Approximately 4.3% of women and 0.6% of men surveyed in the Pentagon study said that they had been the victim of a sexual assault.
Compared to 2014, the military said that this represents an estimated decrease of about 1,000 sexual assaults of women and 4,300 assaults of men.
Officials did not provide a single reason for the decrease in assaults but noted enhanced efforts at communication, prevention and an institutionalization of policies aimed at countering assault.
Officials also noted a 1.5% increase in the number of victims of sexual assault who said they reported their assault through the appropriate channels.
The report's findings, which are based on answers provided by of over 150,000 anonymous respondents, also found that the number of cases where disciplinary action was taken had also increased.
The report said that commanders had sufficient evidence to take disciplinary action in 64% of cases. And of those cases, 59% resulted in court-martials. Members of Congress and outside groups have criticized the military in the past for relying on the chain of command to prosecute sexual assault cases.
But Pentagon officials, while noting improvements, said that more work remained.
"We do not confuse progress with success," acting Assistant Secretary of Defense for Readiness Elizabeth Van Winkle told reporters at the Pentagon.
"Sexual assault violates the core values of our military and must never be tolerated," Rear Adm. Ann Burkhardt, the director of the Sexual Assault Prevention and Response Office, told reporters.
Outside groups welcomed the overall decrease in sexual assaults but called for additional measures to improve accountability and end retaliation.
"The drop in prevalence is a step in the right direction, but the military still has a long way to go in ending the epidemic of rape and sexual assault, holding assailants accountable, preventing and punishing retaliation, and eradicating rampant misogyny and harassment within the ranks," Protect our Defenders, an advocacy group focused on combating sexual assault in the military, said in a statement.
In 2004, the Defense Department created the Care for Victims of Sexual Assault Task Force to address a rise in reports of assault. A need for a more centralized and comprehensive task force led to the creation of the Sexual Assault Prevention and Response Office in 2005. The surveys began in 2006.
While this year's survey showed a drop in sexual assaults, it found little change in the numbers of reported incidents of sexual harassment, with that figure exhibiting no significant decrease from 2014 to 2016.
"Sexual harassment is an area where we need to make further progress," Burkhardt said.
Instances of sexual harassment, including the Marines United scandal have gained increased attention, with each of the services taking action in an attempt to tackle the issue which has been complicated by the rise of social media.