It’s been four years since two female students accused a U.S. Naval Academy teacher, Marine Maj. Mark Thompson, of having sex with them amid a drunken night of strip poker at his Annapolis home.

The flawed investigation that followed — closely examined in a story this week by The Washington Post — shined light on one incident among several that have deeply embarrassed the nation’s service academies in the past two decades. In 2003, a survey revealed that one in 10 women at the U.S. Air Force Academy had been sexually assaulted while attending the school. In 2006 and again in 2014, members of the U.S. Naval Academy football team were acquitted of rape charges. In 2013, the U.S. Military Academy was humiliated by its rugby team after leaked emails revealed rampant misogyny.

But military leaders have in recent years tried to address problems of sexual misconduct at the three prestigious academies, and new government data indicates they may have made progress. The total number of reported sexual assaults, according to the Department of Defense, nearly tripled in the past seven years, peaking at 91 during the 2014-2015 school year. Women made 80 of those reports and men made 11.

Though the spike could imply to some that the number of assaults has increased, the department said in a January report that the figures indicate a “growing trust in the reporting system.”

“We’ve seen a lot of the progress we expected to see when [then-Defense Secretary Chuck Hagel] last year ordered the superintendents to take sexual assault prevention and response programs under their direct supervision,” said Nathan W. Galbreath, senior executive advisor for the department program created to address the problem military-wide.

Each of the academies saw an increased number of reports in the most recent school year: the Naval Academy had 25 (up 9 percent over the previous year); the Military Academy had 17 (up 55 percent); and the Air Force Academy had 49 (up 96 percent).

A Defense Department review pointed to a number of specific tactics that officials believe has contributed to the apparent progress:

• The Naval Academy obligates coaches and members of its athletic teams and clubs to sign a code of conduct contract that requires them to abide by “expected behavior standards and to represent the Academy in the best possible manner.”

• The Military Academy’s superintendent meets with cadets once a month in an open forum to get feedback on the school’s climate, discuss its sexual assault-prevention program and listen to concerns.

• The Air Force Academy hosts regular sessions with members of its sports teams, where they can discuss dating and relationship issues with mentors and experts trained in dealing with sexual assault.

Still, the government report made clear that problems persist.

Nearly 300 cadets, midshipmen and academy staff members participated in a series of focus groups, and those involved indicated that students sometimes “react negatively” when they learn that a classmate has reported a sexual assault.

“Participants suggested that sometimes,” the report said, “those who report can be excluded from social acceptance, criticized both publicly and privately, and have their credibility challenged.”

The accuser in the 2013 Naval Academy case described being treated like a pariah by classmates as she was left in “complete and total isolation” on campus.

Those comments echo ones made by the student who accused Maj. Mark Thompson of raping her in 2011. (He was acquitted of the assault charge but convicted of five lesser offenses.)

At his court-martial, the woman told jurors she didn’t immediately report the alleged incident because she feared it would jeopardize her career in the military and her reputation at the academy.

“I didn’t really want to talk about it,” she said. “I just wanted to leave it alone.”