The nation’s three elite military colleges reported a record number of sexual assault cases this year, according to a Defense Department report issued Friday, prompting calls inside and outside the Pentagon for more aggressive steps to reverse the trend.

Military officials argued that the increase could be reflective of a changing culture that makes victims increasingly willing to report the crimes, but senior Defense officials and activists said the cases are nevertheless an unacceptable blemish at institutions that groom the country’s most promising leaders in uniform.

“I am concerned that we have not achieved greater progress in preventing sexual assault and sexual harassment among academy cadets and midshipmen,” Defense Secretary Leon E. Panetta wrote to the chiefs of the Army, Navy and Air Force. “These crimes and abhorrent behavior are incompatible with the core values we require of our Armed Forces’ future officers.”

The military academies reported 80 cases of sexual assault, a 23 percent increase from the last academic year.

All but four of the individuals who reported having been assaulted during the 2011-12 academic year were women, a figure that senior military officials said could be misleading, noting that men are extraordinarily reticent to report having been victims of sexual assault. More than 60 percent of the assaults were reported by personnel assigned to the Air Force Academy in Colorado Springs, which had a 33 percent increase compared with the previous year.

The new figures follow a report about pervasive sexual abuse and inappropriate conduct by trainees at Lackland Air Force Base in Texas, the service’s main instruction facility. That report, released last month, said that at least 48 female students were victims of sexual assault or inappropriate conduct by instructors between October 2010 and June 2011.

Advocates for military victims of sexual assault said Friday’s report is evidence that the military has a long way to go to overcome cultural and legal barriers that stand in the way of holding perpetrators accountable.

“This report shines a light on the severity and scope of the crisis,” Nancy Parrish, president of Protect Our Defenders, an advocacy group, said in a statement Friday. “It validates our worst fears and what we know to be true because of the number of frantic calls and emails we receive for active duty personnel who continue to be retaliated against for reporting their rape.”

Maj. Gen. Gary Patton, the director of the Pentagon’s Sexual Assault Prevention and Response Office, told reporters in a conference call Friday afternoon that military officials view the increase in reports as a “positive trend,” because it suggests military personnel feel empowered to seek help and justice.

“It means there is a victim that is receiving some sort of care,” he said.

Patton said many victims of sexual assault remain reticent to speak out, a challenge military leaders are trying to address through overhauls in training and case management.

Military officials said that there were four convictions for sexual crimes in court-martials during the academic year. Many other cases were not prosecuted because victims were not willing to confront their alleged aggressors in military courtrooms.

Anu Bhagwati, the executive director of the Service Women’s Action Network and a former Marine Corps captain, said more women would likely be willing to report crimes if they could get cases before civilian courts, an option that is not currently available.

“The criminal justice system is not designated to serve victims,” she said. “It is designated to protect the wrongly accused.”