Keith Towler said concern about the possibility of a cover-up by powerful people was understandable and insisted a full investigation was the only way to resolve the issue.
The intervention came after a victim of the north Wales care home scandal criticised the way the original Waterhouse Inquiry was conducted.
The tribunal, led by Sir Ronald Waterhouse, the advocate and judge who died last year, heard evidence from more than 650 individuals who had been in some 40 homes between 1974 and 1990, and published its report in 2000.
However, Steve Messham, who says he was abused by a leading Thatcher-era Conservative politician – who has not been named – said the terms of reference meant he was not able to raise abuse that took place outside the care system.
News that Mr Towler is to write to the First Minister of Wales, Carwyn Jones, to request the inquiry came as campaigning Labour MP Tom Watson said he aimed to speak out about the allegations of child abuse "in the highest places" despite threats to his safety.
The MP and Labour chairman, who helped expose the phone-hacking scandal, claimed trusted sources had told him he would be at risk if he decided to "dig any deeper" into the claims, which he raised in the House of Commons last month.
Mr Watson tweeted: "I just want to say thank you for the very kind expressions of support. It means a very great deal. Will report back more when I can."
It came as Culture Minister Maria Miller said a public inquiry could be held into the Jimmy Savile sex abuse scandal if the BBC's own investiga- tions failed to reveal the truth about the Top of the Pops and Jim'll Fix It presenter's behaviour.
Sir Ronald had ruled at the time of the inquiry that any living person who was accused or likely to be accused of abusing children in the North Wales homes could not be named, unless they had previously been convicted of such an offence.
Mr Towler said yesterday: "I would support a full inquiry.
"The fact that we have someone on camera now who was clearly a victim of appalling abuse in Bryn Estyn children's home back in the 1970s and 80s, saying that what he wanted to say was outside of the terms of reference, and people told him that he could not say these things and he couldn't talk about people who had abused him, is clearly wrong.
"The fact that he is now saying that and he has now said it so publicly means we have to respond to that."
He said the suggestion of a cover-up raised concerns that had to be addressed.
"The only way that we can clearly put that to bed is to say, at the top of the tree, we will conduct that inquiry and we will allow that inquiry to go as far as it needs to go.
"Unless you do that, that level of suspicion will always be around that there is a cover-up."
The late Leonard Rossiter became the latest star name to be implicated in the growing scandal that erupted in the wake of the claims about Savile.
It was alleged at the weekend that the star of Rising Damp was involved in an attempted sex attack on a teenage male extra in the late 1960s.
The claim emerged following a week in which Gary Glitter and Freddie Starr were questioned by police investigating sex abuses.
Radio 4 presenter Jonathan Dimbleby has claimed there is now a "witchhunt" against the BBC.
Meanwhile, all traces of graffiti that had been daubed on the cottage owned by Savile in Glencoe have been removed.