Mr Towler told the BBC News Channel "What Steve Messham is telling us are... there are things he wanted to say... that for one reason or another, he wasn't able to say... if there are issues there for the police to investigate, then that needs to be investigated."
He said he would be writing to the first minister in Wales "as the children's commissioner to say... I'm concerned about what Steve Messham is saying and I want to make sure a full inquiry takes place to make sure that the evidence that he wants to give can be given."
On the claims surrounding the politician, who has not been publicly named, Mr Towler said: "Sometimes when people move to protect individuals or institutions, they do so at the expense of victims and that is unacceptable."
A Downing Street spokesman said: "Allegations of crimes should be reported to the police and fully investigated.
"If someone is concerned that an allegation was reported in the past but not fully investigated, they should raise this with the police or relevant authority so that they can look again at what happened."