An Air Force officer who runs the Sexual Assault Prevention Unit is now charged with sexual battery for allegedly groping a woman. David Martin reports. (CBS)

The Pentagon estimated Tuesday that 26,000 members of the military were sexually assaulted last year, 36 percent more than a year earlier, in a trend so severe that senior officials warned it could threaten recruiting and retention of military personnel.

President Barack Obama, reacting to the startling figures, said he has "no tolerance" for sexual assaults in the ranks and pledged to crack down on commanders who ignore the problem. Obama said he had spoken to Defense Secretary Chuck Hagel and ordered that officers "up and down the food chain" get the message.

"I expect consequences," Obama told reporters at the White House. "If we find out that somebody's engaging in this stuff, they've got to be held accountable — prosecuted, stripped of their positions, court-martialed, fired, dishonorably discharged, period. It's not acceptable."

News of the drastic increase in both reported and suspected sex crimes — and assertions that many women in the military fear retaliation if they report an assault — comes as the Pentagon struggles to maintain balance with a shrinking budget after more than a decade of wars overseas.

It also comes two days after police in Arlington, Va., arrested the chief of the Air Force sexual assault prevention branch after he was accused of groping a woman outside a bar near the Pentagon. Officials said Lt. Col. Jeffrey Krusinski was removed from his post after the arrest.

The numbers are a blow to the Pentagon's military and civilian leaders, who have pledged to curb sexual assaults and repeatedly announced initiatives to combat the problem, only to see reported rapes and other assaults continue to rise.

"This department may be nearing a stage where the frequency of this crime and the perception that there is tolerance of it could very well undermine our ability to effectively carry out the mission and to recruit and retain the good people we need," Hagel said at a Pentagon news conference. "That is unacceptable to me and the leaders of this institution."

In March, Baltimore native Brian Lewis, 33, was one of four former service members to testify before a Senate Armed Services subcommittee on the challenges of reporting rape in the military. He told the panel that after he was raped by a fellow Navy sailor, he was ordered to keep the incident quiet.

On Tuesday, Lewis said the report "shows a failure of leadership all the way from the White House to the lowest-level commanders" and "really demonstrates the need for aggressive reform."

Lewis said he felt sexual assault had "never been taken seriously" by the military. He said many of those who did not report assaults are men.

"It's my experience, and I know I'm not alone," he said. "I know 26,000 are joining me every year."

After helping to unravel a sexual assault scandal at Aberdeen Proving Ground in the 1990s, retired Maj. Gen. Robert D. Shadley was unsurprised by the abuses documented in the Pentagon report.

The increase in the number of sexual assaults — the Pentagon estimated that about 19,000 members of the armed forces were assaulted the year before — was surprising, Shadley said, adding that the military has done little to address the issue over the years.

"I have been monitoring this since 2000, when I left the military, and I have seen no significant improvement in the last 13 years," Shadley said.

Shadley wrote a book about his experience at Aberdeen called The GAMe: Unraveling a Military Sex Scandal, with the name based upon a "game" in which, he said, senior instructors at an Aberdeen school would try to see how many trainees they could have sexual relations with.

More than 50 female trainees complained of sexual misconduct ranging from rape to prohibited consensual sex in 1996 and 1997. The scandal led to the suspension of 12 instructors, some of whom were later convicted and imprisoned.

After the complaints began at Aberdeen, other women stepped forward at training bases around the country and in Europe, saying that they also had been victims of sexual misconduct.

Shadley said he worked to try to uncover the extent of the sexual misconduct and offer solutions, but he also received a reprimand because he was a commander at Aberdeen when the assaults occurred. His proposed solutions, which include removing sex offenders, better treatment of victims and changing the military culture to make sexual assaults reviled, have been ignored, he said.

"Aberdeen was painted as an aberration," he said. "I believe that the Army wanted to protect the image and not portray itself as having a severe problem, and as a result, we didn't really make significant strides in reducing the problem."

Shadley speculated from the 26,000 victims estimated in the Pentagon report that there were likely 8,000 perpetrators involved in multiple assaults. Out of 1.3 million members of the military, Shadley said, the number of perpetrators is relatively small, but tarnishes the whole organization.