Queensland's Assistant Police Commissioner Mike Condon says Brett Cowan was never dismissed as a suspect in the disappearance of Daniel Morcombe.
Former detective Dennis Martyn told the coronial inquest into Daniel's 2003 death on Wednesday that Mr Condon told him to "f*** off, you wouldn't know anything" when he said he believed Cowan was the man responsible.
His former police partner, Kenneth King, also testified he had considered Cowan a key suspect but the Major Incident Response team did not immediately pursue their lead.
Mr Condon told the inquest the conversation with Mr Martyn never took place, a claim he reiterated outside court on Thursday.
Mr Condon denied the conversation ever took place in his evidence on Wednesday.
"That's an outrageous remark," Mr Condon told the inquest.
Outside the court on Thursday he said that: "Up until the point of his conviction he (Cowan) was never dismissed as a suspect.
"Those officers at that time did a good job, they made the inquiries as they were asked.
"Their reasons for making those comments are only known to them."
Cowan was convicted in the Brisbane Supreme Court in March 2014 for abducting and murdering 13-year-old Daniel more than 10 years earlier.
His arrest came after an elaborate sting operation involving police from three states coaxed him into confessing to undercover officers, who he believed were gangsters.