The Daily Camera says former Boulder District Attorney Alex Hunter believed he didn't have enough evidence to prosecute the case.
"Hunter did the right thing," 9NEWS legal expert Scott Robinson said. He says signing the indictment would have compromised any future prosecution of a possible intruder.
The Ramsey's and their adult son were cleared of any wrongdoing in 2008 by the Boulder District Attorney Mary Lacy.
Robinson does say Colorado law is unclear as to whether a prosecutor can refuse to sign off on an indictment.
"What Hunter did was an equivalent to a pocket veto," Robinson said.
JonBenet was a 6-year-old beauty queen when she was found bludgeoned and strangled in the basement of her parents' Boulder home just after Christmas in 1996.
Robinson in a previous interview said he's not sure there's much anyone can do in advancing the case with the absence of new DNA evidence or a verifiable confession from the killer.
"The case is as cold as cold can be," he said.