WASHINGTON—After years of concern over sexual assault in the military, the Defense Department has proposed the most far-reaching reforms to its justice system in decades.

The proposal, introduced with little notice in late December, would fundamentally change the way America’s men and women experience justice while in uniform.

“It’s a potential sea change,” said Charles Erdmann, the chief judge of the U.S. Court of Appeals for the Armed Forces, the military’s highest court. “These would be the biggest reforms in 30 years.”

For the first time, the Pentagon would issue sentencing guidelines for military crimes. All convicted service members would have a right to appeal. Military judges would determine sentences, replacing a power long held by juries made up of soldiers with little or no legal experience.

But Congressional critics of the military justice system noted that neither the legislation, nor the 1,300-page review that prompted it, addressed a fundamental issue: the role of commanders.

In courts martial, senior commanders decide whether to press charges, select juries and in some cases provide clemency for troops under their command, raising concerns about the impartiality of prosecutions.

“It is telling that a supposedly holistic review of the military justice system completely ignores the role of the commander,” said Sen. Kirsten Gillibrand, a Democrat from New York who has battled with Pentagon leaders over changes to its code. “Until we reform the foundation of the military justice system to remove bias, all efforts to fix its shortcomings will be incomplete.”

Some Congressional insiders are skeptical of the military’s intent. If the Pentagon manages to obtain approval for the bill, it will be harder to make a case for further changes, such as removing military commanders from making decisions on criminal cases. There is also doubt about the bill’s chances. It’s a complex piece of legislation moving through the Hill during an election year. Key players among Republicans and Democrats who have supported the Pentagon on military justice issues have yet to weigh in on the proposal.

A Pentagon spokesman said the proposed legislation did not address the issue of the commanders’ role because a previous Congressionally established panel recommended no changes.

“The current review focused on measures to improve the current process rather than on revisiting the underlying fundamental policy,” said Army Lt. Col. Joe Sowers, a Department of Defense spokesman.

Military leaders hallow their justice system. First adopted during the Revolutionary War, some parts have existed unchanged for more than 200 years. Even today, sailors can be put on a diet of bread and water for minor infractions of the Uniform Code of Military Justice.

The code is a means to convey both justice and military discipline. For instance, soldiers can be tried for going AWOL (punishable by up to 18 months in prison and a dishonorable discharge) or for disrespecting an officer (up to one year in prison and a bad conduct discharge).

They can also face trial for crimes ranging from kiting checks to rape and murder. Military courts can try soldiers for crimes that have no direct connection to military service — a soldier assaulting a local resident during an off-base bar fight, for example. Commanders argue that they need such power to ensure order and discipline in military ranks.

Over the decades, military leaders have wrestled with the tension inherent in the system. The last big overhaul resulted from complaints during World War II when, all told, more than 1.7 million troops were tried in courts martial. Soldiers fighting for democratic freedoms found themselves subject to a judicial system that many felt was arbitrary and unjust.

“At the end of the war, many people were mad as hell,” said Fred L. Borch, III, a historian for the Army’s Judge Advocate General’s Corps and former chief prosecutor for the Guantanamo military commissions. “No matter what they did or what they said, they were found guilty.”

The current proposal comes after years of controversy over the military’s handling of sexual assault.

“The Invisible War,” a 2012 documentary, provoked outrage after finding that active duty female soldiers serving in combat zones were more likely to be raped by a comrade than killed by an enemy.

A year later, in a closely watched case, Air Force Lt. Gen. Craig Franklin vacated a court martial conviction of a subordinate officer for sexually assaulting a civilian medical worker, prompting a review by then-Secretary of Defense Chuck Hagel.

In 2014, the most recent year for which data is available, a survey estimated that nearly 19,000 service members had been subjected to “unwanted sexual contact.” That compared to 6,131 official reports of sexual assault that year. About 1,600 cases resulted in some sort of action for sexual assault violations.

The Defense Department responded with a barrage of blue-ribbon commissions and fact-finding bodies. Congress imposed more than three dozen changes to the military codes for sexual assault.

Rape victims now have the right to a special attorney to represent them in court. Their sexual histories cannot be used by defense counsel. Most significantly, military commanders were stripped of their abilities to dismiss sentences in felony cases, including sexual assault.

But senior military officials feared that many of the changes focused on sex crimes without regard to the rest of the system. For instance, survivors of attempted murder or aggravated assault do not have guaranteed access to a special representative in court. In addition, there were concerns that the system had tipped in favor of victims over the accused.

In 2013, Hagel approved a “holistic review” of the entire military justice system. Andrew Effron, a former chief judge, was appointed to lead the effort.

The result addressed many long-standing concerns. Unlike in civilian courts, military juries determine both guilt and the sentence for an offender. But the members of the panel, enlisted men and officers picked by the military officer who convened the court martial, are not required to have any legal training. The Pentagon proposal would give military judges a more central role, allowing them to determine punishments and discharges.

In addition, the Pentagon plan would set out typical minimum and maximum punishments over the coming years to provide guidance to judges. And the size of military juries — which can vary from five people to 15 or more — would be standardized.

The reforms also provide that all offenders can appeal their convictions — a right previously guaranteed only to those who received more than a year in prison, or a punitive discharge.

Don Christensen, president of Protect Our Defenders, a group dedicated to improving military handling of sexual assault, acknowledged that the proposed changes were far-reaching.

But the central issue of the commander’s influence, he said, remained untouched.

“There’s a debate raging in the halls of Congress and the media and it’s not addressed,” said Christensen, the former chief prosecutor for the Air Force. “That’s a problem.”