Owens' comments came Wednesday as he announced his decision not to appoint a special prosecutor to look into the 1996 death of the six-year-old beauty pageant winner.
He said after initial mistakes, police and prosecutors are working with new evidence and headed in the right direction.
"During my own review of the Ramsey case," Owens said, "I've learned that substantial new evidence -- including evidence that did not originate in the grand jury proceedings -- is presently being analyzed and will continue to be analyzed by the prosecution team."
The governor, though, had strong words for the girl's parents.
"If I could speak to John and Patsy Ramsey," Owens said, "I would tell them to quit hiding behind their attorneys, quit hiding behind their PR firm. Come back to Colorado and work with investigators in this case, no matter where that trail will lead."
Early on Dec. 26, 1996, Mrs. Ramsey told police she found a ransom note demanding $118,000 for her daughter's safe return. Eight hours later, JonBenet's father said he found his daughter's body in the basement.
Critics contend the investigation was compromised when detectives allowed the Ramseys and friends to roam through their mansion in Boulder.
Owens said the guilty parties have been smart, stonewalling police and covering their tracks.
The Ramseys, who moved to the Atlanta area after the killing, have insisted they are innocent. In a statement issued late Wednesday, the Ramseys' attorneys called Owens' remarks "slanderous."
"Coming from a public official elected to the highest office of this state, his comments are unconscionable," the statement said.
"To the killers, let me say this: You only think you have gotten away with murder. There is strong evidence to suggest who you are," Owens said. "I think investigators are moving closer to proving their case. They will keep pursuing you. You will reap what you have sown."
Owens declined to comment when asked if he was referring to the Ramseys when he cited more than one killer. He wouldn't say if he believed the Ramseys were involved in their daughter's death.
Two weeks ago, a Boulder County grand jury completed a 13-month investigation of the death without issuing any indictments. District Attorney Alex Hunter said there was not enough evidence to charge anyone, though he and police said the Ramseys remain under suspicion.