Hagel's order came after the Army announced a sergeant who served as a sexual harassment and assault prevention officer at Fort Hood in Texas is being investigated for sexual misconduct, The Washington Post reported. Ten day ago, an Air Force lieutenant colonel in charge of sex assault prevention was arrested in Virginia on a charge of groping and battery.
The sergeant's name has not been released because he has not yet been charged. Officials say he has been suspended from duty, and sources told the Post he is also suspected of forcing a woman to prostitute herself.
Under Hagel's order, thousands of people will have to be screened a second time, recertified and retrained in dealing with sexual assaults.
"I cannot convey strongly enough his frustration, anger and disappointment over these troubling allegations and the breakdown in discipline and standards they imply," George Little, the Pentagon press secretary, told reporters.
Reaction on Capitol Hill was swift Tuesday night.
"Tragically, the depth of the sexual-assault problem in our military was already overwhelmingly clear before this latest highly disturbing report," said Senate Armed Services Committee Chairman Carl Levin, D-Mich.
His committee will act next month on a number of measures to address sexual assault in the military, Levin said.
Committee member Kirsten Gillibrand, D-N.Y., said she would introduce legislation Thursday to change military law to make independent prosecutors, not commanders, responsible for handling sex crimes and other serious offenses. Military leaders have resisted such proposals.
House Armed Services Committee Chairman Buck McKeon, R-Calif., said he was "outraged and disgusted" by the allegations and said his faith in the military to police sex crimes was "deeply shaken."
Eleven days ago Lt. Col. Jeffrey Krusinski, in charge of the Air Force's sexual abuse prevention programs at the Pentagon, was arrested not far from his Virginia office for allegedly drunkenly groping and battering a woman in a parking lot.
Krusinski faces a trial in July for sexual battery.
He has been removed from his job, and his arrest drew condemnation from Hagel and President Barack Obama.
Lawmakers expressed outrage last month in two cases in which Air Force generals granted clemency to convicted sex offenders.
The Pentagon released a report last week estimating the number of military personnel who have been sexually assaulted or victimized by related crimes surged some 35 percent over two years despite intensive efforts to confront the problem.