Army Brigadier General Jeffrey Sinclair leaves the courthouse at Fort Bragg in Fayetteville, North Carolina, on March 4, 2014. (Ellen Ozier/Reuters)

The sexual assault case against an Army general was thrown into jeopardy Monday when the judge said the military may have improperly pressed ahead with the trial to send a message about its determination to curb rape and other widespread sexual crimes and misconduct.

The judge, Col. James Pohl, ­refused to dismiss the charges against Brig. Gen. Jeffrey A. Sinclair but offered the defense another chance to plea-bargain the case down with a different set of military officials.

The twist comes with the Pentagon under heavy pressure from Congress and the public to combat what the military says is an epidemic of rape and other sex crimes.

Pohl reviewed newly disclosed e-mails in Sinclair’s case and said he found evidence of unlawful command influence in Fort Bragg officials’ decision to reject a plea deal before the trial began last week.

Under the military code of justice, the decision was supposed to be made solely on the evidence, not its broader political implications.

The defense has until Tuesday morning to decide whether to submit a plea-bargain proposal again or allow the court-martial to proceed.

Sinclair, the 51-year-old former deputy commander of the 82nd Airborne Division, is accused of twice forcing a female captain to perform oral sex on him in Afghanistan in 2011 during a three-year extramarital affair. He has admitted to the affair but denied assaulting the woman.

He is believed to be the highest-ranking U.S. military officer ever court-martialed on sexual assault charges. He could get life in prison if convicted.

Richard Scheff, the general’s lead defense attorney, would not say how he might proceed.

“This is an unprecedented situation,” Scheff said. “It’s a mess created by the government. It wasn’t created by us. We have so many options, we don’t even know what they all are,” he said.

Military prosecutors had no comment after the hearing.

Before the trial, Sinclair had offered to plead guilty to some of the lesser charges in exchange for the Army dropping the sexual assault charges, but he was turned down.

A key issue is whether the rejection was influenced by concerns about the message it would send across the military. A letter by the attorney for Sinclair’s accuser that raised the concerns was discussed in e-mails between a high-ranking Washington-based Army lawyer, the prosecutors and the commanding general overseeing the case.

Pohl said he doesn’t think the whole case was tainted, just the decision on a plea agreement.

The judge also criticized prosecutors for not giving defense attorneys the e-mails sooner: “The only reason we are in this conundrum is because of the government’s late notice,” he said.

The Pentagon has estimated that as many as 26,000 military members may have been sexually assaulted in 2012, based on an anonymous survey.

Meanwhile, the Senate appeared to be headed toward a vote in favor of big changes in the military justice system to deal with sexual assault, including scrapping the nearly century-old use of the “good soldier defense” to raise doubts that a crime had been committed. Currently, those accused of wrongdoing can cite their good military records.

— Associated Press