WASHINGTON — When President Obama proclaimed that those who commit sexual assault in the military should be “prosecuted, stripped of their positions, court-martialed, fired, dishonorably discharged,” it had an effect he did not intend: muddying legal cases across the country.       

In at least a dozen sexual assault cases since the president’s remarks at the White House in May, judges and defense lawyers have said that Mr. Obama’s words as commander in chief amounted to “unlawful command influence,” tainting trials as a result. Military law experts said that those cases were only the beginning and that the president’s remarks were certain to complicate almost all prosecutions for sexual assault.       

“Unlawful command influence” refers to actions of commanders that could be interpreted by jurors as an attempt to influence a court-martial, in effect ordering a specific outcome. Mr. Obama, as commander in chief of the armed forces, is considered the most powerful person to wield such influence.       

The president’s remarks might have seemed innocuous to civilians, but military law experts say defense lawyers will seize on the president’s call for an automatic dishonorable discharge, the most severe discharge available in a court-martial, arguing that his words will affect their cases.       

“His remarks were more specific than I’ve ever heard a commander in chief get,” said Thomas J. Romig, a former judge advocate general of the Army and the dean of the Washburn University School of Law in Topeka, Kan. “When the commander in chief says they will be dishonorably discharged, that’s a pretty specific message. Every military defense counsel will make a motion about this.”       

At Shaw Air Force Base in South Carolina last month, a judge dismissed charges of sexual assault against an Army officer, noting the command influence issue. At Fort Bragg in North Carolina last month, lawyers cited the president’s words in a motion to dismiss the court-martial against Brig. Gen. Jeffrey Sinclair, who is accused of forcing a lower-ranking officer to perform oral sex on him, among other charges.       

In Hawaii, a Navy judge ruled last month that two defendants in sexual assault cases, if found guilty, could not be punitively discharged because of Mr. Obama’s remarks. In Texas, a juror was dismissed from a military panel on a sexual assault case after admitting knowledge of the president’s words. In Alexandria, Va., Eric S. Montalvo, a former defense counsel in the Marine Corps who is now in private practice, has cited the president’s words in motions to dismiss two sexual assault cases, one against an Army sergeant and the other against a Navy seaman.       

“Because the president is the commander in chief, it’s going to come up in basically every imaginable context in sexual assault cases,” said Eugene R. Fidell, who teaches military justice at Yale Law School.