Acting Defense Secretary Patrick Shanahan called for tougher action against sexual assault in the US military Thursday after an annual Pentagon report said the number of assaults in 2018 had risen from recent years.

Sexual assaults reported by Defense Department employees, both men and women, jumped 13 per cent last year to 7,263 compared to 2017.

Moreover, actual sexual assaults were likely to be about triple the reported number, given the estimate that just one out of three victims in the military file a complaint.

"It is clear that sexual assault and sexual harassment are persistent challenges," Shanahan said in a statement.

"To put it bluntly, we are not performing to the standards and expectations we have for ourselves or for each other. This is unacceptable."

Based on a survey taken only every two years, the report said that not only the number but the prevalence of sexual assault was on the rise in 2018. 

Around 6.2 per cent of women in the Department of Defense experienced sexual assault or unwanted sexual contact in 2018, compared to 4.3 per cent two years earlier, according to the report. 

The level for men was much lower and relatively stable: 0.7 per cent experienced assault in 2018, slightly higher than 0.6 per cent two years ago.

The problem was worst in the Marines: some 10.7 per cent of women in that service reported sexual assault last year, compared to 7.5 per cent in the Navy and lower rates in the other services. 

Sexual assaults on men from all services was in the 0.7-0.8 per cent range.

Shanahan said he supported a proposal to seek a specific crime for sexual harassment under the military's unique justice system.