The Office of the Children's Commissioner is concerned about Oranga Tamariki's new Hear Me, See Me campaign.
The $2 million campaign launched a year ago, tells young people's stories online in a bid to make New Zealanders care more.
Two youth organisations have pulled out of its advisory group, saying their views were marginalised by the ministry.
A Children's Commissioner spokesperson said the office had "expressed some concerns to the group about the process of engagement".
"Our specific concerns relate to the process for engaging with mokopuna voices and the purpose and objectives not being clear."
They said it would continue to work with the group "as appropriate".
RNZ has asked for more details of the Children's Commissioner's concerns.
Oranga Tamariki said earlier it apologised if it had not addressed concerns raised "as effectively as we could have" and would welcome the chance to rectify this.
On Friday it said it was "working with the OCC directly to ensure any concerns raised are being addressed in full".