For more than a year, U.S. military officials have admitted they have a serious problem with sexual assault and harassment in the ranks. They’ve pleaded with the White House, Congress and the public to trust commanders to fix it on their own terms.

But the Pentagon’s argument has been undercut badly by fresh reports of senior commanders bungling cases or coming under investigation themselves.

On Wednesday, the Navy acknowledged it had reassigned the former commander of its elite Blue Angels flight squadron after it received a complaint that he had tolerated sexual harassment, hazing and lewd behavior.

On Tuesday, The Washington Post reported that a two-star Army general had been suspended because he had failed to notify criminal investigators, as required, of a sexual-assault complaint against a colonel with whom he worked closely. Last month, the Army was forced to cut a plea deal with a brigadier general being court-martialed on sexual-misconduct charges after a judge found evidence that political pressures may have influenced the case.

The embarrassing episodes surfaced soon after the Senate narrowly defeated a bill in March that would have stripped commanders of their authority to oversee the prosecutions of sexual-assault cases and other major crimes. The Pentagon had lobbied heavily against the measure. The close vote delivered a warning that lawmakers’ patience with military leaders was wearing thin.

“We’ve had a constant cry from the military saying, ‘Trust us,’ ” said Sen. Kirsten Gillibrand (D-N.Y.), the lead sponsor of the bill, which would have given military prosecutors the power to press charges and ended commanders’ ability to influence cases. “But there is no standard under which commanders are being held accountable, and it’s amazing.”

Gillibrand said she would try to bring her bill to another vote this year, but she added that she wished the White House would intervene. “I also hope the president’s paying attention,” she said Thursday in a phone interview. “He could make this change all by himself.”

President Obama has stood by the Pentagon but also has told military leaders that they need to “step up their game exponentially” on the issue. He has said the Defense Department must show progress by December or he will consider “additional reforms,” an allusion to Gillibrand’s proposal.

Nancy Parrish, president of Protect Our Defenders, an advocacy group that represents sex-crime victims in the military, said the recent scandals could easily sway votes in Congress.

“We know that there were a number of senators who were really just on the fence . . . and that they just wanted to give the Pentagon a little more time,” she said, referring to the vote in March. “But the continual drip, drip, drip of these cases, I’m sure, will change the political calculus.”

Under the military justice system, commanders have the final say on which cases go to court-martial. The commanders also can modify sentences or impose punishment in cases that do not go to trial.

Military leaders say diminishing those powers would undermine commanders’ authority. They note that commanders, not uniformed prosecutors, are responsible for upholding order and discipline in their units and ensuring the welfare of their troops.

Gen. Mark A. Welsh III, the Air Force chief of staff, said commanders closely heed the advice of military lawyers anyway. He said an internal analysis of Air Force court-martials over a three-year period showed commanding officers accepted prosecutors’ recommendations in all but a handful of cases.

“So the idea that the commanders aren’t trained, and therefore you don’t take the right action, is an interesting discussion, but it’s not true,” Welsh said Wednesday at the National Press Club. “It just doesn’t happen. And so that logic doesn’t track well with me.”

At the same time, military officials have acknowledged that many victims don’t report sex crimes because they don’t trust their commanders or the broader military justice system to protect them from reprisals.

The armed forces have devoted lots of energy and resources to trying to make their current system work. They have expanded training sessions and counseling programs. Commanders talk frequently about the importance of preventing sexual crimes and punishing perpetrators.

Some leaders, however, have acknowledged that those efforts may turn out not to be enough.

“We’ve been given about a year to demonstrate both that we will treat this with the urgency that it deserves and that we can turn the trend lines in a more positive direction,” Army Gen. Martin E. Dempsey, chairman of the Joint Chiefs of Staff, told reporters April 11.

But, he added: “If it occurs that after a period of very intense and renewed emphasis on this that we can’t solve it, I’m not going to fight it being taken away from us.”