The troopers, who were cleared of criminal charges in the case, had moved to block an internal state police review into the December 2007 incident.
They claimed it could violate their right to privacy.
But U.S. District Judge Mary Cooper said the state police's investigative arm can question the troopers about what happened.
Noting that the alleged victim claimed she was raped, Cooper wrote that the right to privacy only protects consensual sexual contact.
Cooper also noted that the state police already regulates troopers' on-duty and off-duty conduct, so the agency's investigative arm has the authority to probe whether the trooper's conduct violated any of those regulations.