Gillibrand's office said the senator, a member of the Armed Services Committee, took the unusual move against Obama, a fellow Democrat, because she was "extremely troubled" by Rooney's justification of why she didn't like Gillibrand's proposal to remove the chain of command from decisions to prosecute allegations of sexual assault and other major crimes in the military.
Rooney, tapped by Obama to be the Navy's No. 2 civilian, told the Armed Services Committee ahead of her confirmation hearing her justification had to do with the limits of evidence in the military.
"A judge advocate outside the chain of command will be looking at a case through a different lens than a military commander," Rooney said in a statement. "I believe the impact would be decisions based on evidence rather than the interest in preserving good order and discipline."
Basing decisions solely on evidence would be bad because "I believe this will result in fewer prosecutions and therefore defeat the very problem that I understand it seeks to address," she said.
Gillibrand said it was "shocking statements like those of Jo Ann Rooney that further erode" the trust sexual-assault victims place in the system.
"The United States legal system is based on evidence, justice and due process," Gillibrand said in a statement first reported by Capital New York.
"Why isn't this good enough for our service members who risk everything to protect those freedoms?" Gillibrand said.
"The brave men and women we send to war to keep us safe deserve nothing less than a justice system equal to their sacrifice. If you were a service member raped on duty, why would you have confidence to come forward and report after hearing that basing decisions to prosecute solely on evidence would be a bad outcome?" Gillibrand said.
"Jo Ann Rooney's testimony should send chills down the spine of any member of the armed services seeking justice," she said.
Rooney, currently principal deputy undersecretary of defense for personnel and readiness, said after her original comment she never meant to suggest military commanders shouldn't weigh the evidence when deciding whether to prosecute sexual-assault allegations.
"My original answer expresses the view that commanders must evaluate more than the evidence," Rooney said in a letter to Armed Services Committee Chairman Carl Levin, D-Mich.
Other considerations for commanders include morale and discipline within the ranks and the possibility of "non-judicial punishment."
The White House had no immediate comment on Gillibrand's hold on the nomination, which will require Rooney to receive 60 votes for confirmation.