Most Rev Justin Welby claimed he did not see the same "integrity" from the BBC in response to its own failures concerning Savile, compared to action by the Church.
Speaking on BBC Radio 4, he said: "I haven't seen the same integrity over the BBC's failures over Savile as I've seen in the Roman Catholic Church, in the Church of England, in other public institutions over abuse.
"We may be proved wrong about that..."
A BBC spokesman said it didn't recognise the "characterisation" made by Archbishop Justin. They pointed out the corporation published the full details of an independent investigation following the scandal.
Speaking with BBC News, they added: "We set out very clear actions to ensure the highest possible standards of child safeguarding."
A spokeswoman for Lambeth Palace said the Church of England fully accepts its own failures in the area of safeguarding, adding that Archbishop Justin's been clear protecting the young and vulnerable should be the church's "highest priority".
Highlighting the creation of the Church's National Safeguarding Team in 2015 and new policies, she added: "The Archbishop believes this level of rigorous response and self-examination needs to extend to all institutions, including the BBC."