The number of sexual-assault complaints within the ranks was 3,553 between January and September, up from 2,434 reports in the same period last year, the Pentagon said.
"We assess this as a sign of victim confidence in our response system," Pentagon spokeswoman Lt. Col. Catherine Wilkinson told USA Today.
A Defense Department slide highlighting the figures was less definitive. It said the increase in assault reports "may reflect a change in victim confidence in Department of Defense response systems."
All U.S. service branches reported increases in sexual assault reports, the Pentagon said. The service branches are the Army, Navy, Marine Corps, Air Force and Coast Guard.
Reports of sex assaults are a fraction of Pentagon estimates of unwanted sexual contact among troops, from groping to rape.
The Defense Department said in May as many as 26,000 military members were sexually assaulted last year, up 37 percent from 2011's 19,000.
Those figures led to outrage expressed on Capitol Hill and among top Pentagon officials.
Defense Secretary Chuck Hagel ordered reforms to reduce the number, and lawmakers started crafting measures intended to bolster the military justice system's response to assault reports.
A bipartisan-supported bill sponsored by Sen. Kirsten Gillibrand, D-N.Y., could be debated next week.
It proposes removing commanders from the process of deciding whether sexual misconduct cases go to trial. Instead, that authority would be given to independent military prosecutors who hold the rank of colonel or higher.
The Pentagon is against the measure, saying sexual-assault prosecutions must stay with military commanders to maintain good order and discipline.
Gillibrand's bill has 47 senators publicly behind it, but will likely need 60 votes to pass, Senate Armed Services Committee Chairman Carl Levin, D-Mich., told reporters this week.
He said the higher vote count would probably be needed because the measure was controversial.
Gillibrand welcomed the Pentagon report Thursday but disputed its conclusion about why the number of reported sexual assaults was up.
"Without additional data on the total number of estimated assaults during this period, or the number of cases prosecuted by commanders, it is impossible to make any conclusions," she said in a statement.
"That said, increased reporting is a good thing, but we need increased reporting, lower incident rates and increased accountability after someone reports. That's why we must create an independent military justice system so that when more service members do report they will have a fair shot at justice," Gillibrand said.