As an Army general faced court-martial for sexual assault this month, a military lawyer sat each day in the front row of the gallery, a few feet behind the prosecutors.

Unlike lawyers trying to win a criminal conviction against Brig. Gen. Jeffrey A. Sinclair, Capt. Cassie L. Fowler’s sole mission was to protect the woman at the center of the case — a captain who said her commander twice forced her to perform oral sex and threatened to kill her if she told anyone about their three-year affair.

Known as a special victims counsel, or SVC for short, Fowler is part of a program started by the Pentagon last year after long-standing complaints that the military has too often treated those reporting rapes and sexual assaults as if they were the ones who did something wrong.

Officials say they hope the SVCs will help victims navigate the complexity of the military justice system and provide support.

In the months since the program was expanded to all military branches, the new corps of about 200 handpicked and specially trained lawyers has represented hundreds of soldiers, sailors, Marines and airmen as the alleged perpetrators were investigated, tried and, in some cases, convicted.

Gen. Ray Odierno, the Army’s top commander, has met with some of the sexual assault victims.

“Here’s the message I’m getting from them: ‘The best thing we’ve done is the victim advocates,’ ” Odierno said earlier this month. “It’s clear to me that the victims are feeling much more comfortable with these special victim advocates, and I’m dedicated to ensuring we carry out this program within the Army.”

Among the early successes: An Air Force SVC representing a female airman successfully fought to remove a mark from the woman’s service record placed there in retaliation for reporting her sexual assault. In another case, an SVC informed a commander that an officer overseeing an evidentiary hearing had acted improperly in recommending dismissing charges against the accused. The commander overruled the officer and sent the case to court-martial.

The counsels have had to fight for acceptance in a military justice system that can be slow to accept change. SVCs have reported threats of retaliation when challenging decisions or conduct of a higher-ranking officer. Internal e-mails released as part of the Sinclair case show that senior Army lawyers privately ridiculed the assigned SVC.

At issue was a letter Fowler sent in December that helped persuade the top general at Fort Bragg to reject a plea deal that would have dropped the sexual assault charges against Sinclair. Fowler suggested that to do otherwise would “have an adverse effect on my client and the Army’s fight against sexual assault.”

Col. Michael Lacey, the senior military lawyer at Fort Bragg, e-mailed a subordinate that he didn’t like Fowler. The other Army lawyer then replied that Fowler was “very preachy.”

“Exactly and I don’t worship her god,” Lacey responded.

Military court watchers said Fowler’s letter stated the obvious — that the resolution of the case against the highest-ranking officer ever charged with sexual assault will be closely watched. However, the judge overseeing the case later cited the letter as evidence the commander had been improperly influenced by the potential political fallout if he had agreed to dismiss the charges.

Judge Col. James Pohl’s ruling set the stage for Sinclair’s lawyers to renegotiate a deal with the government. Sexual assault counts against him were dismissed recently in exchange for guilty pleas on lesser charges. Sinclair’s punishment? A reprimand and a $20,000 fine.

Fowler was not authorized to comment for this story, but her boss said he supports her handling of the case “100 percent.”

“Every SVC is charged to zealously represent their client, even when that interest is not in the government’s interest,” said Col. Jay McKee, who has managed the Army’s SVC program since its Nov. 1 launch.

The SVCs were introduced as the U.S. military was rocked by the often chilling details of sexual assaults within the ranks. In May, a Pentagon survey estimated that up to 26,000 military members may have been sexually assaulted in 2012, though less than 3,400 reported those incidents to superiors.

Sen. Kirsten Gillibrand (D-N.Y.), who has been among the most outspoken congressional critics of the military’s handling of sexual assault cases, said that SVCs have told her privately that they sometimes advise victims not to report, especially if they were drinking at the time of the incident. SVCs also have advised clients against seeking mental health treatment, urging them to speak to a chaplain instead to protect those private conversations and keep them out of court.

Although the rules for military trials have not yet clearly defined SVCs’ participation, Gillibrand said she will seek broader authority for them.

“Having an advocate for every victim is very meaningful, but they need a meaningful role within the legal system and that is something we need to keep working on going forward,” she said.

Recently, a captain who was raped expressed her gratitude to her SVC before a panel created by Congress to review the military’s response to sexual assault cases.

The Associated Press does not publish the names of sexual assault victims.

The rapist is serving a 25-year prison sentence. The captain remains on active duty.

“The best description that can be made is that a court-martial is like a chess game,” she said. “The defense and the prosecution are the people making the moves and the victims are just chess pieces that don’t know the overall plan. The SVC was able to support me while the prosecution and defense were moving their chess pieces.”