Roger Meekings, who carried out a 2009 past case review for the Diocese of Chichester, told the Independent Inquiry into Child Sexual Abuse that information about clergy who were later jailed had not been in their personnel files.
They included former Bishop of Lewes Peter Ball and Canon Gordon Rideout, both of whom were later imprisoned.
He told the London hearing into abuse in the Anglican church that the so-called "blue files" on staff were also often missing Criminal Records Bureau (CRB) check data.
He said he had been told "the previous bishop had a habit of 'filleting' the blue files".
Public hearings are taking place this week to examine how the religious order handled paedophilia allegations stretching back to the 1950s, first focusing on Chichester.
Such sexual abuse may have thrived in the Anglican church due to an "excessive emphasis" on forgiving offenders in its ranks, the inquiry earlier heard.
Ball was jailed for 32 months in 2015 for abusing boys. But 22 years previously, in 1993, he was investigated and let off with a caution for gross indecency by police after abusing a trainee monk.
The inquiry heard that a 470-page correspondence file on Ball existed.
But Mr Meekings, a former social worker and ex-head of children's services in East Sussex, said that although it had run to 290 pages at the time of his reports, what he had been shown had not been "anywhere near" that large.
It included a letter written by Rev Brian Tyler, a former police officer, after the 1993 arrest.
In the letter, the inquiry heard on Thursday, Mr Tyler said: "Unfortunately, I have come to the conclusion he (Ball) has been involved in not only abusing his office but even young men who passed through his care.
"He desperately needs help."
Asked whether he would have acted differently if he had seen the letter, Mr Meekings told the inquiry: "My conclusion was that action needed to be taken.
"But I think I would have given a heightened action to it, perhaps a flashing red light around it."
He was also asked about the file he reviewed on Rideout, who was jailed for 10 years after he abused more than a dozen girls and boys at a now closed Barnardo's home in Crawley, West Sussex, over a four-year period.
Mr Meekings told the inquiry: "I have a memory of receiving it, and there having been nothing of concern in it."
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