IT was the winter of 1987.

I'd just become the BBC's Scottish political correspondent and was used to working odd hours. But when the phone rang at 5am, I was more than unusually tetchy. "You'd better get down here," said the news desk. "Special Branch has just raided Queen Margaret Drive and it looks like they're going to arrest half the management under the Official Secrets Act."

The raid was over an untransmitted documentary in the Secret Society series, produced by journalist Duncan Campbell for the BBC in Scotland, which disclosed the existence of a secret £500 million spy satellite programme called Project Zircon. For the next 28 hours the BBC was in turmoil. Film editors were forced to identify every can of relevant film. It ultimately led to the resignation of one of the BBC's most celebrated director generals, Alasdair Milne.

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So I find it hard to agree with BBC world affairs editor John Simpson that the Savile affair has been the corporation's worst crisis in 50 years. I was working in the BBC 17 years after Zircon, when the institution was plunged into what really was its worst crisis – the Hutton Report into the death of weapons inspector Dr David Kelly. Hutton accused the BBC of "editorial failure" in allowing the Today reporter, Andrew Gilligan, to remark that the dossiers on Iraqi weapons of mass destruction had been "sexed up".

It led to the resignation of another celebrated BBC director general, Greg Dyke, along with the chairman of the board of governors, Gavyn Davies. Out of the door with them went a lot of the BBC's independence and editorial self-confidence. The BBC bureaucracy was shattered and the corporation has since become timid and defensive.

Which may explain why the Savile affair has probably been the worst-handled crisis in the BBC's history. From the moment the story broke, no-one seemed able to take charge. Incorrect blogs remained uncorrected; BBC journalists attacked each other; an independent inquiry was announced too late; and everyone from the director general down seemed more interested in covering their own backsides than exposing Savile. New boss, George Entwistle, who gloried in the name "head of vision", has shown a demonstrable lack of it.

Watching his performance in Westminster was painful – and worrying for anyone who values public service broadcasting. The editor-in-chief of the world's greatest broadcasting organisation came across like a local authority bureaucrat caught not meeting his targets in the leisure and recreation department.

Politicians don't like broadcasters at the best of times – they feel they give them a bad public image – so some MPs leapt at the opportunity to turn the tables and do a Jeremy Paxman on the BBC boss.

They guffawed when he said he "did not want to do anything that demonstrated excessive interest" in one of the most explosive stories the BBC has ever covered. Entwistle appeared to dump the blame on the one person who couldn't answer back: the editor of Newsnight, Peter Rippon, who took the decision to spike the story. Excuses have been made for Entwistle's performance: he's new to the job; MPs were grandstanding. True. But that doesn't alter the fact he appears unable to conduct himself competently in a public forum.

It is a measure of the BBC's failure that it has become the story, not the revelations about Savile's sordid travels. The victims seem to have been forgotten. Had the corporation acted swiftly and openly, this need not have been a crisis but an opportunity for the state broadcaster to take a lead in exposing one of the great untold scandals of our times.

And if the BBC is in the dock, so is the UK press. With all their sources in the entertainment world, the tabloid newspapers cannot have been unaware of the allegations about Savile. Thousands of journalists and private investigators are paid large sums of money to expose the dark side of celebrity life. Savile's sex abuse of disabled children would have been a massive story – the kind of story, surely, the now defunct News of the World would have died for in its heyday.

Savile was a friend and confidant of royalty, and a great giver to charities. But the press had no qualms about exposing private conversations of a sexual nature between Prince Charles and Camilla Parker Bowles, so why would it go to such lengths to protect him?

The material acquired by the Newsnight journalists, including Liz McKean, should have been broadcast – even though it was the testimony of "just the women" as Rippon described Savile's victims in that unfortunate email. Was Rippon leaned on by his bosses? Did they tell him to back off? I doubt it. The BBC takes editorial freedom seriously and is reluctant to appear to censor its journalists.

I fear it may be worse than that. The culture in BBC journalism is now so risk-averse, editors probably don't need to be told when to back off. They don't want the story to get in the way of a good career.

It's safety first at the BBC now – but being a safe pair of hands isn't what you need in an editor or a director general. You need forceful personalities who can lead, inspire and encourage independent and courageous journalism. Without that, the BBC is not worth the licence fee. With newspapers in decline, and people turning to the internet for news, the BBC has perhaps become too influential. Its increasing dominance in online journalism might be acceptable if it could be relied upon to be as independent, investigative and informative as newspapers are at their best. We need a BBC that causes trouble and speaks truth to power, to use the current cliche. But I'm not sure the BBC is in the trouble-making business any more – at least while it is in the hands of bureaucrats who seem to see their main function as deflecting blame.

I can't imagine today's BBC risking prosecution under the Official Secrets Act by making programmes about secret spy satellites.

What happens now? Entwistle may not survive the report from the Select Committee. If MPs accuse him of failing in his editorial responsibilities or worse, passing the buck, his position might become untenable. Rippon has yet to give his side. There will be arrests and that could lead to more publicity.

The corporation is going through the institutional equivalent of a nervous breakdown. You can almost hear the ghost of Savile laughing.