Credit: J. Scott Applewhite/AP Photo

Sen. Claire McCaskill, D-Mo., today defended her belief that it's essential to keep military commanders involved in the prosecution of sexual assault cases, which she called a "very difficult and embarrassing and critical problem."

Standing in front of retired female officers, McCaskill stressed the need to keep them as part of the process, despite an opposing bill from fellow Democratic Sen. Kirsten Gillibrand of New York that calls for military sexual assaults to be removed from the military chain of command and transferred to local civilian prosecutors.

McCaskill noted that she talks "all the time" to Gillibrand and they are "joined at the hip on all of the very aggressive reforms that are in this bill," but it's an "honest difference of opinion" between the two on this one.

"This boils down to whether or not you should remove all of the major criminal justice issues away from the command structure totally, and have just the lawyers making the decision," McCaskill said at a news conference on Capitol Hill. "I think we're going to continue to disagree on it."

McCaskill's legislation calls for commanders to retain the power to refer cases for court-martial. But if commanders decline to pursue cases, there will be a review by civilians in the armed service branches.

Gillibrand wants to remove the decisions from the chain of command and set up a separate and independent prosecutor's office to handle sexual assault cases. She argues that would increase reporting and reduce the fear of retaliation.

McCaskill, a former prosecutor, said she believes there "will be even more" that she and Gillibrand will "agree [with] on the floor, but this particular one - that somehow turning this all over to the lawyers and letting the command wash their hands of it - I would never agree to that unless I really believed it was going to be better for victims. And these women and the victims I've talked to and my experience as a prosecutor tells me it will not be."

In a passionate defense of her proposal, joined by Democrat Sen. Jon Tester of Montana and Republican Sen. Kelly Ayotte of New Hampshire and several retired female officers, McCaskill repeatedly said that keeping the cases within the chain of command is the "best way to protect victims and realize more aggressive and successful prosecutions," although she also kept returning to the point that victims would be able to choose to report outside of the chain of command.

"We believe that there will be less retaliation, we believe there will be more prosecutions," McCaskill said. "We believe that the only way to hold command accountable is to make them responsible, not to completely remove their responsibility. We believe that's a recipe for disaster."

Ayotte agreed, saying, "what this comes down to is we cannot let commanders off the hook."

"Everything within the military happens within the chain of command, and if we take away the responsibility of commanders, to make sure that victims are supported, to make sure that these cases are vigorously prosecuted," Ayotte said. "If we take it away from them then we are also taking away the responsibility to act. It is hard to ask someone to be accountable for a failure to act when you take away responsibility to act."

Gillibrand's legislation has high-profile bipartisan support, as well. Both Sens. Rand Paul, R-Ky., and Ted Cruz, R-Texas, have signed on to her proposal.

The issue of sexual assaults in the military came to the forefront on Capitol Hill recently after a series of sex-crime scandals in the military earlier this year, as well as the release of a Pentagon report in May showing a six percent increase in the number of reported sexual assaults last year.

Tester noted that the "commanders in the field" are already "directing people in life and death situations" and "we put full confidence in them to make decisions."

"There is no reason, there is no reason why we shouldn't continue to place that confidence in them in the sensitive issue of military sexual assault," Tester said.

McCaskill said anyone who thinks she could be trying to block prosecutions has it completely wrong, although she acknowledged that the narrative that has developed between the competing legislation is that it has been "victims versus the uniforms" and she said, "that's just not true."

"I think anybody who knows my record, who knows that I've been working at this for years, who understands my time in a courtroom, no one in the Senate has cried with more victims of sexual assault than I have," McCaskill said. "No one has looked more juries in the eye and said, 'Put this man in prison for as long as the law allows.' No one has had more experience with these kinds of crimes than I have. The notion that I would ever be a roadblock to prosecutions, is enough to give me a stomachache."

Retired Marine Col. Ana Smythe, a 31-year veteran, gave a passionate defense of keeping the military chain of command involved in prosecutions, saying that while she acknowledges there is a problem, "the essence of the military is built, that structure is built around the chain of command."

"That's where the authority is, that's where the trust is, the confidence is in that commander," Smythe said. "He has to uphold the honor and that he put in by taking his oath of office that was his responsibility. When you take command that command is, is the essence of everything you have been taught since the day you walked in the Corps. If we dismantle or weaken the chain of command, we are lost. How can you possibly take out of the chain of command away from the commander, the authority for criminal action? That's part and parcel of what you are assigned to do from day one."

Col. Lisa Schenk, who was the one member of the Army JAG Corps at the event, said she prosecuted sexual assault crimes, as well as worked as a victim liaison. She agreed that change is needed, but called for a "thoughtful approach to change."

"If you take out the command authority from the process, you are essentially gutting the military justice process," Schenk said. "You have to look at why they are there in the first place. They are there for discipline and our military justice process is for discipline. Victims need to be empowered and this bill empowers the victims."

ABC News' Joan Greve, Alisa Wiersema, and Arlette Saenz contributed to this report.