The report, which was released Monday after an 18-month investigation, is based on interviews with more than 150 male and female victims of sexual assault, as well as a review of military documents.
The Pentagon reported earlier this month that 62% of troops who reported being sexually assaulted last year indicated that they had been subjected to some form of retaliation.
Military members reported being subjected to threats, vandalism, harassment, poor work assignments, loss of promotion opportunities, disciplinary action and criminal charges, according to Human Rights Watch.
"The US military’s progress in getting people to report sexual assaults isn’t going to continue as long as retaliation for making a report goes unpunished," said Sara Darehshori, senior US counsel at Human Rights Watch and co-author of the report. "Ending retaliation is critical to addressing the problem of sexual assault in the military."
Those who retaliate, however, are rarely held accountable or punished.
Since 2012, the Pentagon inspector general, which investigates instances of retaliation, has closed two cases without substantiating the charges. It has three open cases, a department spokeswoman told USA Today.
"When no one is held accountable for retaliation, it creates a hostile environment for all survivors, and sends a message to criminals that they can act with impunity" said Don Christensen, president of Protect Our Defenders and former chief prosecutor of the US Air Force.
He continued: "When a survivor who reports sexual assault is 12 times more likely to suffer retaliation than they are to see their rapist convicted, it demonstrates the military has a long way to go in fixing this problem."
Major General Jeffrey Snow, who leads the Pentagon's sexual-assault prevention and response programs, said military leaders are drafting a strategy to deal with retaliation. Among the proposals is a confidential tip line.
"The first thing in addressing any issue is to acknowledge you have got a problem," Snow said in an interview with USA Today. "And clearly we have done that and have taken steps. And we'll stay after it."
In 2014, there were about 20,000 incidents of what the military refers to as unwanted sexual contact – a 27% decline from 2012. Those incidents range from groping to rape. Nearly two-thirds of women who reported assaults also indicated they had been subject to retaliation. There was not enough data on men to draw conclusions.
Human Rights Watch said the Military Whistleblower Protection Act, which was enacted to protect service members from employment-related retaliation, has yet to help a single service member whose career was harmed, despite the prevalence of the problem.
The agency called on Congress to strengthen the law to give service members the same level of protection as civilians.
