Auditor-General Mike Blake said that there were questions about the quality of the selection panel's report that Ms Thorp used to make the decision.

However, he said that there was no evidence of bias from the panel, which chose to dump incumbent Paul Mason and recommend Aileen Ashford as the new commissioner.

"Despite limitations of the selection report, there is persuasive evidence of a thorough, logical and objective selection process," he said.

"(But) given the minister's effective responsibility for making the appointment, she should have asked the panel to more fully explain its reasoning."

Mr Blake also recommended the Children's Commissioner's term be extended beyond the current three years.

He said that having three members of the selection panel from agencies scrutinised by Mr Mason was not ideal.

"The panel was selected despite advice from DHHS that recent selections for similar positions in Queensland, New South Wales and Western Australia had avoided including panellists from entities with a direct relationship with the commissioner," the report said.

Ms Thorp welcomed the Auditor-General's findings.

"Since the appointment of Aileen Ashford I have had to repeatedly defend the integrity of that process," she said.

Ms Thorp highlighted a section of the report that noted her role was also "free from bias".

Opposition Leader Will Hodgman said that the vagueness of the selection panel's report showed a cloud still hung over Ms Thorp.

He said that Ms Thorp had not properly examined the facts.

Premier Lara Giddings said that the report exonerated Ms Thorp and said that the issue could now be put to bed.

Mr Mason said that if Ms Thorp had rejected the panel's decision and reappointed him then she would have avoided any accusations of political bias.