Navy medical spokesperson Shoshona Pilip-Florea acknowledged that unintended pregnancy rates had been high, but the Navy's own surveys had "noticed the trend" and implemented programs to address the problem.
"It has a huge impact on mission readiness, especially as we are changing to a defense where women can serve and it becomes even more important to enable them to protect themselves," she told ABCNews.com.
Pilip-Florea says that the Ibis survey is based on data that is five years old and many changes have been underway since 2008.
The Navy's own data shows that the number of unintended pregnancies is now "closer to the general population" -- at about 6 percent, according to Pilip-Florea.
The Navy's Sexual Health and Responsibility Program now provides pre-deployment education on birth control and family planning, in accordance with a campaign by the Department of Health and Human Services to combat unintended pregnancies.
Navy surveys show women had a wide variety of reasons for not using birth control which contributed to an unintended pregnancy: 1 in 4 said she was "not sexually active," according to Pilip-Florea.
"These data suggest that women who are not currently in a relationship may not feel the need for birth control, and that it's important for health educators and clinicians to help young women think about the benefits of being ready when and if she does become involved in a sexual relationship," she said.
Pilip-Florea also said many young women have an "old perception" about the use of long-acting reversible contraceptives like an IUD and the injectable hormone Depo-Provera. At one time, the IUD was not given to women who had not previously had children, but new recommendations have changed that.
Other young women are misinformed about the reliability of the birth control pill, which must be taken at the same time each day, or condoms, which can break.
Popular forms of contraception, like the "ring," also have to be refrigerated, which can be difficult when serving for months at a time on a ship.
"The study cited a couple of instances of misinformation and fear of reprisal, but from the Navy's perspective, we believe it is central to the equipment of our sailors and Marines to protect against unwanted pregnancies for mission readiness," said Pilip-Florea.
Since December 2012, Navy policy requires that women are offered contraceptive services before they receive their orders for operational duties.
Service members usually get three to six months between time of orders and actual deployment, allowing "ample time to stabilize" and physically adjust to their chosen form of birth control," said Pilip-Florea. The Navy also provides a long-term supply of birth control pills, for example, including "a couple of months extra."
ABCNews.com contacted the Army for comment, but did not get an immediate response.
Advocacy groups have pushed for legislation to give women better access to birth control and to abortion, according to Greg Jacob, policy director for the Service Women's Rights Action Network (SWAN), whose mission is to secure equal opportunities for active-duty military women and veterans.
The Department of Defense now gives women access to the so-called "day after pill," Plan B, which is available over-the-counter at medical treatment facilities.
SWAN also supported the 2011 March for Military Act, sponsored by Sen. Kirsten Gillebrand, D-New York, which pushed for lifting the ban on elective abortions at military hospitals, but was not enacted.
But the very nature of military life and its chain of command can make obtaining birth control onerous," said Jacob.
"They allow you to go to the hospital, but you have to ask permission," he said. "Particularly with the younger troops, they have to check with a platoon sergeant, get a pass, and get a chit that says what you were treated for and what your duty status is, and turn that in. The system is in place for millions of people to be accountable, but the level of privacy is not the same as in civilian life."
Women have access to regular preventive care, but educating military doctors to ask a woman if she is sexually active or needs birth control is important, he said.
Jacob suggested the military look to universities as models for educating about reproductive services. "It's the same sort of demographic -- young people in a restrictive controlled environment," he said.
Jacob said the end of the longstanding ban on women serving in combat will have a positive effect in empowering young women.
Over the years, critics of full integration have argued that men and women serving in combat could be distracting and create a "sexually charged atmosphere." But Jacobs said the new policy will go a long way to end sexual assault and, as a consequence, some unintended pregnancies.
The military already has strict rules forbidding sexual relationships between fellow soldiers, according to Jacob. "They have all the tools in place for dealing with issues of behaviors."
"From a harassment and an assault perspective, one of the key things we have found is the issue of the two-tiered second-class soldier culture," he said. "By fully integrating the troops and members feeling a part of the team, that type of behavior is reduced."
For Jacob, who served 10 years in the Marines, overseeing and reporting to women, a fully integrated military raises standards for all.
"Some of the women who I worked with are the best Marines I ever served with," he said. "My philosophy is there should be one standard for the Marines, not a separate one for men. It raises the entire performance standard of the regiment."