An investigation by the police in Charlottesville, Va., and an internal inquiry ordered by the state attorney general’s office may ultimately lead to the truth in the University of Virginia case. As of Monday, the police department acknowledged it had started an investigation, but would not elaborate.

The fallout from the article reflects just how complicated dealing with sexual assault can be — from identifying a crime to protecting the rights of both the accusers and the accused. The vast majority of sexual assaults on campuses are not reported. When they are, victims must navigate a byzantine system that often discourages the involvement of the police. Those who make the claims —as well as the accused — often feel the system does not mirror legal courtrooms in which decisions are made by impartial, outside arbiters.

“We have a legal system that has grown up over centuries that people have absorbed as part of the culture that entails an impartial judge,” said Eugene R. Fidell, an expert on military justice at Yale Law School. “There is formality, dignity and power of the state for both sides — victims who have been assaulted and the accused.”

Mr. Lowry said that putting the onus on colleges to handle such cases, as most federal legislation does, will have negative effects. “It’s a real mistake for colleges and universities to come up with these processes,” he said. “That doesn’t offer protections for the defendants and does not have punishment for the guilty.”

Experts on sexual assault cases say a lack of focus remains on the underlying causes of assaults, including binge drinking, which federal data shows has increased on college campuses in recent years, and other cultural and demographic factors. “The fact that both the college experience and the military experience are often the first time people of this age range are independent, have access to alcohol and are interacting socially with members of the opposite sex,” said Victor M. Hansen, the associate dean at New England School of Law in Boston, “suggests to me that we have not done enough before young people reach this age to educate, model and encourage appropriate behavior.”

Conservatives, liberals and advocates agree, however, that the Rolling Stone article has complicated the picture for rape victims going forward. “Our concern is that young women around the country who may have been inspired by this story and empowered to speak up about their own personal experiences will hesitate to engage with journalists on a subject as painful and complex as this one can be,” said Marsha Robertson, a spokeswoman for Futures Without Violence, a women’s advocacy group. “And that would be a tragic repercussion.”

The article continued to affect universities across the country. A large group of students plan to protest Michigan State University’s decision to allow the conservative columnist George Will to speak at its winter commencement after he wrote in The Washington Post that some campus rape survivors have achieved a “coveted status” of “victimhood.”