The Westminster strand of the Independent Inquiry into Child Sexual Abuse heard that civil servants were wary of Savile's activities as far back as 1984.
The inquiry saw letters between then-head of the Honours Committee and Margaret Thatcher's secretary resisting calls for Savile to be knighted despite pressure from the prime minister.
Lord Robert Armstrong cited interviews with Savile published in the Sun the previous year where he boasted about having people beaten up, sleeping with hundreds of girls and giving recommendations to a suicidal man on how to take his own life.
-> Met Office issues yellow weather warning for snow to Yorkshire"My committee did not feel that sufficient time has elapsed since Mr Savile's unfortunate revelations in the popular press in April of this year," Lord Armstrong said.
"He is much in the public eye and it is unlikely that the lurid details of his story will have been forgotten. I fear it would be best if Mr Savile were to wait a little longer."
He also refused to include him in the birthday honours list, saying: "The lapse of time has served only to strengthen the doubts felt about a knighthood for Mr Savile.
Lord Armstrong added: "Those of whom I have consulted now consider that a knighthood for Mr Savile would give rise to enough unfavourable comment to risk bringing the honours system into disrepute"
In response to Mrs Thatcher's attempts to have Savile knighted in 1987, Lord Armstrong again highlighted the interviews in the Sun, adding that in the light of the Aids crisis, his "sexual promiscuity" was a problem.
In 1998, the Honours Committee received an anonymous letter referring to "reports of a paedophilia nature" could emerge about Savile and allegations about his involvement with rent boys.
It said: "While within limits and bounds homosexuality can be rationalized in a modern society, we must not lose sight that paedophilia goes beyond any boundaries which right-minded people of whatever political persuasions find abhorrent."
Giving evidence, senior civil servant Helen MacNamara - who currently heads the Honours and Appointments Secretariat - said that such a letter would now immediately be passed to the police.
She said that as Savile had been knighted in 1991, the letter would have prompted further inquiries about whether the case should be brought before the forfeiture committee.
Ms MacNamara said she did not know how the letter was dealt with at the time or if any concerns were raised with the authorities.
The inquiry previously saw documents between senior civil servants relating to MP Cyril Smith, who was investigated for child abuse, and former high commissioner to Canada Peter Hayman who was suspected of being involved in the Paedophile Information Exchange.
They recommended that the men be "given the benefit of the doubt" or be "spoken to" warning them about their future conduct.
As a result, Smith was knighted while Hayman was not stripped of his honour.
When asked if criticism of the honours system for protecting itself rather than considering victims was fair, Ms Macnamara replied: "That's absolutely a fair criticism."
She said that in the wake of various scandals a much more thorough process had been established before individuals are considered for honours, including background checks.
Ms MacNamara added that the Honours Committee was much more likely to err on the side of caution when making nominations.
She said the forfeiture committee now met more regularly to consider those who should be stripped of their honours.
"It is important these cases are considered properly, not least because of the impact on the people," she said.
She added that at the moment, there are no plans to strip people of their awards posthumously, saying: "Honours are a living award. You are a member of the honour while you are alive, and once you are dead the honour dies with you."
But Ms MacNamara said that depending on the recommendations of the inquiry, this could change in future.
The Westminster strand of the far-reaching inquiry is expected to last three weeks and is due to conclude on March 22.