WASHINGTON — President Obama’s nominee for a top civilian job in the Navy is in the crosshairs of female senators determined to overhaul the military justice system to stanch the increasing number of sexual assaults.

Jo Ann Rooney, tapped to be undersecretary of the Navy, responded to a Senate panel last month and offered her opinion on a proposal to remove commanders from the process of deciding whether serious crimes, including sexual misconduct cases, go to trial. That judgment would rest instead with seasoned trial lawyers who have prosecutorial experience and hold the rank of colonel or above.

“A judge advocate outside the chain of command will be looking at a case through a different lens than a military commander,” Rooney said. “I believe the impact would be decisions based on evidence rather than the interest in preserving good order and discipline.”

Sen. Kirsten Gillibrand, D-N.Y., chief proponent of that far-reaching change, was furious and is blocking Rooney’s nomination.

“The United States legal system is based on evidence, justice and due process. Why isn’t this good enough for our service members who risk everything to protect those freedoms?” Gillibrand said, adding, “Jo Ann Rooney’s testimony should send chills down the spine of any member of the armed services seeking justice.”

Rooney sought to clarify her response, writing to the committee on Oct. 16. The nominee said she did not mean to suggest that commanders do not consider evidence. She reiterated her reservations about the proposed change, saying judge advocates would lack the “necessary breadth of perspective” to decide on whether to proceed with a case, especially if they were geographically removed from the accused’s command.

“Even assuming commanders and judge advocates would come to the same conclusions on disposition, it is my opinion that if you remove commanders from decision-making you absolve them of accountability and responsibility for those decisions,” Rooney wrote.

It was clear Wednesday that that answer failed to placate Gillibrand, who told a Capitol Hill news conference that the first answer was unacceptable and the second was Rooney “doubling down” on her initial response.

Sen. Barbara Boxer, D-Calif., said she was shocked by what Rooney wrote, saying “it sickened me.”

While the Senate Armed Services Committee has approved Rooney’s nomination, Gillibrand continues to block the pick, raising doubts about her fate just as the Senate is about to engage in a fierce fight over military policy.

The intensity was evident last week as Gillibrand and Vice President Joe Biden engaged in an animated conversation on the Senate floor on the issue of sexual assault in the military. Biden was in the Senate to swear in Sen. Cory Booker of New Jersey.

On Wednesday, Gillibrand was joined at an emotional news conference by a victim of assault, retired military, advocates and a bipartisan group of senators who back her legislation. She will push to attach her measure as an amendment to the annual defense policy bill that the Senate is expected to consider the week of Nov. 18.

Forty-six senators support the proposal, including 38 Democrats and eight Republicans.

But she is up against the Pentagon and the chairman of the Armed Services Committee, Sen. Carl Levin, D-Mich., as well as fellow female Sen. Claire McCaskill, D-Mo.

Levin – echoing the Joint Chiefs of Staff – wants to keep commanders involved in deciding whether to prosecute sexual assault cases.

Military leaders have argued that removing the decision from their purview would undercut the ability of officers to maintain good order and discipline in their units.

The Pentagon estimated that as many as 26,000 military members may have been sexually assaulted last year, up from an estimated 19,000 assaults in 2011, based on an anonymous survey of military personnel.

While the number of sexual assaults that members of the military actually reported rose 6 percent to 3,374 in 2012, thousands of victims were still unwilling to come forward despite new oversight and assistance programs aimed at curbing the crimes, the report said.

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