The 2013 National Defense Authorization Act, which the president signed into law late Wednesday night, has been assailed by liberals and libertarians for authorizing the indefinite detention of American citizens. But the annual spending bill this year made a different sort of history as well by repealing the generation-long ban on insurance coverage for abortions for members of the armed services who are victims of rape and incest—finally giving those women the guaranteed affordable coverage in those circumstances that federal prisoners, civilian employees, and Medicaid recipients have long received.

New Hampshire’s senior senator Jeanne Shaheen, who introduced the amendment repealing the ban that had been in effect since 1981 (PDF), called the bill's passage an “important step” toward ending a policy that was “blatantly unfair to women putting their lives on the line.” Currently, military insurance only covers abortions performed to save the life of the mother, and military health-care facilities will only perform them to save the life of the mother or in cases of rape and incest. Shaheen’s amendment will let insurance pick up the cost of the procedure in such cases, rather than forcing the woman to pay out of pocket.

Before the bill’s passage, “military women have been in a situation that has not applied to anybody else covered by federal health care,” Shaheen told The Daily Beast earlier this month. “Even if you’re in federal prison and you are raped you can get abortion coverage. That has not been true for military women since the early ’80s.”

Roughly 215,000 women currently serve, making up nearly 15 percent of the U.S. military.

Greg Jacob, the policy director of the Service Women’s Action Network (SWAN), credited the amendment’s passage to a bipartisan coalition, including lawmakers who had served in the military, and a reframing of the abortion access issue as a “service member’s issue rather than a reproductive rights one.

“This isn’t just about abortion. It’s about the three Rs. Ensuring readiness and retention within the military and how this affects recruitment,” said Jacob, who argued that a dramatic increase in reports of sexual assault within military ranks had impacted all three Rs. He credited SWAN and the ACLU with working alongside traditional reproductive-rights heavyweights like Planned Parenthood and NARAL to Republicans on board. He also credited military members turned lawmakers—118 of whom served in the 112th Congress (PDF)—with playing a key role in passing the amendment.

“The strategy we recommended was to have the military reclaim this issue,” said Jacob, a former Marine captain.

Advocates for women in the military applauded the repeal, but noted that significant questions and concerns about the new policy and its implementation remain.

TRICARE insurance provided to service members will now cover abortions in the case of rape or incest, said DOD spokeswoman Cynthia Smith, who declined to elaborate on how the military would assess such claims.

Some abortion opponents have expressed concern that allowing for abortions or abortion coverage in the case of rape or incest would create an incentive for women to falsely report those conditions, a position that entered the mainstream this year when Todd Akin, the Republican Senate candidate in Missouri, ignited controversy and likely cost himself the seat when he suggested that pregnancy rarely resulted from “legitimate rape,” since “the female body has ways to try to shut that whole thing down.”

The high incidence of rape and sexual assault in the military has gained national attention in recent years. There were an estimated 19,000 sexual assaults in 2010, and underreporting of such crimes, always commonplace, “is exacerbated in military settings,” according to SWAN, which estimates that less than 15 percent (PDF) of military sexual-assault survivors in recent years reported their attack.

The group estimates that 65 percent of military pregnancies are unintended (PDF), a rate exacerbated by the low use of contraceptives by female personnel.

Servicewomen who have been sexually assaulted applauded the new rule, but said they were doubtful it would remedy what they see as a broken system, citing the difficulty of reporting crimes within military channels—especially when the assailant is higher up in the chain of command—the stigma accusers faced, and superiors’ frequent protection of perpetrators and mishandling of investigations.

“My biggest concern is that we’re on step one of probably 15,” said victim’s advocate Jessica Kenyon. “The accomplishment is good, but I worry support and understanding will go away.”

Kenyon said she was raped and experienced numerous sexual assaults while training to be an officer, and that the investigations of her assault “were botched from the beginning.” Kenyon was discharged in 2006 for pregnancy after she said a National Guard soldier raped her. Previously, while stationed at Fort Eustis in Virginia, the 31-year-old said she had reported an instructor who had sexually assaulted her, but that her speaking out backfired.

“I watched the whole case unravel in front of me,” she said. “They investigated and found evidence he had assaulted me and other females, but I was the one blamed. He was an instructor that everybody liked so he was put back at his post.”

“The goal of the department is to establish a culture that treats sexual assault as the crime that it is—deterring potential perpetrators and protecting survivors,” the DOD responded in a statement to Keyon’s charge.

Kenyon said that she feared that investigations into charges of rape or sexual assault could, perversely, delay pregnant women from having the now-covered procedure as quickly as they otherwise would. She added that a women who had the procedure without first informing her superior could face retribution for going outside of her chain of command.

“Say a woman gets an abortion and her commander finds out. Say she has a prolife commander. No protection says he cannot make her life a living hell. Retaliatory measures are possible.”

The next step is hammering out clear protocol, and addressing the flawed reporting and investigating practices of sex crimes in the military, says Kenyon, who admits this is no easy feat. She recommends assigning impartial commanders—from units other than the victim’s or accused perpetrators—to hear complaints, or a civilian authority trained in social work.

“I don’t want the repeal of this ban to be another way to make survivors pay for surviving,” said Kenyon, who is a plaintiff in Cioca v. Rumsfeld, one of the class-action lawsuits filed against the Department of Defense charging them with creating an atmosphere allowing rape and sexual abuses to occur and fester.

Shaheen, who has long worked to secure reproductive-rights advances for women, agreed that rape in the military is still a systemic problem, which needs to be addressed, and deemed the repeal of the abortion ban is a small step in that direction.

“We have a long way to go to ensuring policies are carried out across the military,” she said.