Sir Roger Singleton said the Church's Past Cases Review in 2010 did not give a comprehensive picture of the problem and that those conducting it refused to speak to some survivors who wanted to tell their stories.
In public statements, the Church "downplayed negative aspects" of the PCR's findings in order to avoid damaging the reputation of the institution and the then Archbishop of Canterbury, Rowan Williams, said the former Barnado's boss.
But Sir Roger, whose report will be published soon, said he found "no evidence whatsoever of a deliberate attempt to mislead" and no evidence that anyone broke the law.
The PCR looked at more than 40,000 case files relating to allegations of abuse dating as far back as the 1950s and concluded that just 13 cases of alleged child sexual abuse needed formal action.
After survivors complained that the report was inadequate, Sir Roger was commissioned to carry out an independent review of how it was conducted.
He told BBC Radio 4's Today programme that it was "botched in three ways".
"The survey wasn't completely comprehensive," he said. "It didn't include some cathedrals, it didn't include employees working with children in some parishes.
"The attempts really to make the survey absolutely complete were flawed.
"In the public statement that it issued reporting on the review, (the Church) rather failed to give a comprehensive picture of the concerns that existed.
"It narrowed down the definitions of who had actually been responsible for abuse by limiting it to just new cases and cases where the Church took formal action. This had the impact of reducing the numbers from probably nearer 100 to just two which appeared in the public statements."
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