Authorities seized the computer from Karr's home in 2001 and copied the entire hard drive onto paper, including the five illicit images, said Sheriff's Department Lt. Dave Edmonds. He said authorities looked for the computer for the past two weeks, but have had no luck.
"We did an exhaustive search. We have probably hundreds of thousands of evidence items and we're certain at this point, through a couple of weeks of effort, that it's not misplaced inside of our property unit," he said.
Karr, 41, has maintained his innocence in the case.
On Tuesday, prosecutors offered Karr a plea deal that would waive three of the five child pornography possession charges against Karr if he pleaded guilty to the two remaining ones. Karr would get credit for time served, would be placed on probation for three years and would be required to register as a sex offender.
"I wonder if that was the impetus of the offer today," Karr's attorney, Robert Amparan, said. "It seems like a pretty embarrassing mistake for the Sheriff's Department to admit."
Assistant District Attorney Larry Scoufos denied any connection between the missing computer and the plea deal offer.
Karr first made headlines when he was arrested last month after making phone calls and writing e-mails suggesting he killed JonBenet, a six-year-old beauty queen, in her Boulder, Colo., home in 1996.
He was returned to the U.S. from Thailand only to have the Ramsey case collapse when DNA failed to connect him to the crime.