In January, the Welsh Tory leader and the Senedd’s presiding officer clashed after Millar relayed the experiences of abuse survivor Emily Vaughn, who goes under a pseudonym, and who suffered some of the abuse in Wales.
Ms Vaughn later accused Jones of “downplaying” her experience.
Jones said she had been “seeking to protect victims of abuse” and that she was “not sufficiently aware” that Vaughn had spoken publicly before.
Millar said the new inquiry was a “vindication” for Ms Vaughn’s courage and bravery.
A previous independent inquiry into the sexual abuse of children was led by Prof Alexis Jay and reported in 2022.