WASHINGTON — The Pentagon announced Monday that it would ask Congress to overhaul the court-martial system used to prosecute the nearly 5,000 service members annually accused of crimes, scaling back the power of senior commanders to overturn convictions and dismiss charges.

The proposal comes amid sharp criticism from advocacy groups and Congress over how the military has handled a series of sexual assault cases, including a decision by an Air Force commander, Lt. Gen. Craig A. Franklin, to dismiss the conviction of Lt. Col. James Wilkerson, who was found guilty in November of aggravated sexual assault and sentenced to one year in military prison.

“These changes, if enacted by Congress, would help ensure that our military justice system works fairly, ensures due process and is accountable,” Defense Secretary Chuck Hagel said in a statement. “These changes would increase the confidence of service members and the public that the military justice system will do justice in every case.”

Mr. Hagel said that the Pentagon would ask lawmakers to scale back the power of the convening authority — a commander who exercises significant control over courts-martial in a system that dates to the British Empire. The commanders decide whether to approve charges for trial, select the jury and negotiate plea deals, and they can overturn guilty verdicts or reduce recommended sentences.