After hearing submissions, the committee has recommended that as well as a board, a chairperson of the board should be appointed who would be known as the Chief Children's Commissioner.
But the changes do not satisfy Frances Eivers, a former district court judge, who took over the role in November last year.
"I cannot comprehend how the select committee progressed this bill through largely unaltered," she said in a statement.
Of 403 submissions, 311 had vehemently opposed it.
"When such a clear, resonant message is sent to Government, the failure to listen to the people they vowed to represent speaks volumes."
She said removing the power to investigate ran the risk of creating a figure rather than an advocate with real teeth.
She said the Children's Commissioners had been people with real mana such as Dr Russell Wills, Governor-General Dame Cindy Kiro and Judge Andrew Becroft.
"That legacy will end under this new structure and those mokopuna who need the most will be worse off."
While on the surface, the establishment of a "Chief Children's Commissioner" sounded positive the rest of the bill exposed the most vulnerable children to danger from the lack of effective monitoring.
The select committee, chaired by Labour MP Angie Warren-Clark, said it had appreciated concerns about the loss of a clear public-facing identity that children and young people knew and recognised.
"We do not want children and young people to feel that they do not know who represents and advocates for them."
The Green Party submitted a minority report and said the bill should be withdrawn until the final report of the Royal Commission into Abuse in State Care.
The Greens said the bill had been described by the Royal Commission Forum as a deliberate attempt to pre-empt the Commission and was a backwards step masquerading as progress.
"It is rare to consider a bill that has so little community support, and it is particularly disturbing to see so much opposition to a proposal that purports to increase the monitoring of, and advocacy for, the wellbeing of children in care."