The manipulation takes three forms. The first is the attempt to recruit journalists to spy on other people, or to go themselves under journalistic "cover". This occurs today and it has gone on for years. It is dangerous, not only for the journalist concerned, but for other journalists who get tarred with the espionage brush. Farzad Bazoft was a colleague of mine on the Observer when he was executed by Saddam Hussein for espionage. In a sense it didn't matter whether he was really a spy or not. Either way, he ended up dead.

The second form of manipulation that worries me is when intelligence officers are allowed to pose as journalists in order to write tendentious articles under false names. Evidence of this only rarely comes to light, but two examples have surfaced recently, mainly because of the whistleblowing activities of a couple of renegade officers - David Shayler from MI5 and Richard Tomlinson from MI6.

The third sort of manipulation is the most insidious - when intelligence agency propaganda stories are planted on willing journalists, who disguise their origin from their readers. There is - or has been until recently - a very active programme by the secret agencies to colour what appears in the British press, called, if publications by various defectors can be believed, information operations, or "I/Ops". I am - unusually - in a position to provide some information about its operations.

Let us take the third allegation first. Black propaganda - false material where the source is disguised - has been a tool of British intelligence agencies since the days of the second world war, when the Special Operations Executive (SOE) got up to all kinds of tricks with clandestine radio stations, to drip pornography and pessimism into the ears of impressionable German soldiers. Post-war, this unwholesome game mutated into the anti-Soviet Information Research Department (IRD). Its task was ostensibly to plant anti-communist stories in the developing-world press, but its lurid tales of Marxist drunkenness and corruption sometimes leaked back to confuse the readers of the British media.

A colourful example of the way these techniques expanded to meet the exigencies of the hour came in the early 70s, when the readers of the News of the World were treated to a front-page splash, "Russian sub in IRA plot sensation", complete with aerial photograph of the conning tower of a Soviet sub awash off the coast of Donegal. That was the work of Hugh Mooney of the IRD, which was eventually closed down in 1977.

Its spirit did not die, however. Nearly 25 years later, readers of the Sunday Telegraph were regaled with with the dramatic story of the son of Libya's Colonel Gadafy and his alleged connection to a currency counterfeiting plan. The story was written by Con Coughlin, the paper's chief foreign correspondent and it was falsely attributed to a "British banking official". In fact, it had been given to him by officers of MI6, who, it transpired, had been supplying Coughlin with material for years.

The origins of that November 1995 newspaper article only came to light when they were recently disclosed by Mark Hollingsworth, the biographer of renegade security service officer David Shayler. Shayler had worked on MI5's Libya desk at the time, in liaison with his counterparts in the foreign espionage service, MI6, and had come away with a detailed knowledge of events, and a bundle of secret documents to back them up.

The allegations were confirmed from an unexpected direction. The Sunday Telegraph was served with a libel writ by Gadafy's son. The paper was unable to back up its suggestion that Gadafy junior might have been linked to a fraud, but pleaded, in effect, that it had been supplied with the material by the government.

In a long and detailed statement, which entered the public domain in the course of a judgment given in an interlocutory appeal on October 28 1998, the paper described how, under Charles Moore's editorship, a lunch had been arranged with the then Conservative foreign secretary, Malcolm Rifkind, at which Con Coughlin had been present. Told by Rifkind that countries such as Iran were trying to get hold of hard currency to beat sanctions, Coughlin was later briefed by an MI6 man - his regular contact.

Some weeks later, he was introduced to a second MI6 man, who spent several hours with him and handed over extensive details of the story about Gadafy's son. Although Coughlin asked for evidence, and was shown purported bank statements, the pleadings make clear that he was dependent on MI6 for the discreditable details about the alleged counterfeiting scam. He was required to keep the source strictly confidential.

Throughout the formal pleadings, the Telegraph preserved the figleaf of its sources by referring to a "Western government security agency". But this veil of coyness was blown away by City solicitor David Hooper in his book on libel published last month, Reputations Under Fire, in which he says: "In reality [they were] members of MI6."

So, unusually, an MI6 exercise in planting a story has been laid bare. Now, there is no suggestion that Con Coughlin is dishonest in his work. He is a perfectly conscientious journalist who I expect did his best to substantiate his facts and undoubtedly believed in their truth. But nevertheless, those facts may not have been true. And I believe he made a serious mistake in falsely attributing his story to a "British banking official". His readers ought to know where his material is coming from. When the Sunday Telegraph got into trouble with the libel case, it seems, after all, to have suddenly found it possible to become a lot more specific about its sources.

This was not an isolated example of recent MI6 I/Ops. In August 1997, the present foreign editor of the Independent, Leonard Doyle, was also in contact with MI6 while he was at his previous post at the Observer. I know, because I became involved in an MI6-inspired story as a result. Doyle's MI6 contact supplied him with intelligence information about an Iranian exile who, while running a pizza business in Glasgow, was also attempting to lay hands on a sophisticated mass spectrometer which could be used for measuring uranium enrichment - a key stage in acquiring components for a nuclear bomb.

We were supplied with a mass of apparently high-quality intelligence from MI6, including surveillance details of a meeting in an Istanbul hotel between our pizza merchant and men involved in Iranian nuclear procurement.

I should make clear that we did not publish merely on the say-so of MI6. We travelled to Glasgow, confronted the pizza merchant, and only when he admitted that he had been dealing with representatives of the nuclear industry in Iran did we publish an article. In that story we made it plain that our target had been watched by Western intelligence.

Nevertheless, I felt uneasy, and vowed never to take part in such an exercise again. Although all parties, from the foreign editor down, behaved scrupulously, we had been obliged to conceal from our readers the full facts and had ended up, in effect, acting as government agents.

Now, after the Tomlinson/Shayler defections and the subsequent revelation of MI6's continuing I/Ops programme of which my Iranian experience was plainly a part, I think the cause of honest journalism is best served by candour. We all ought to come clean about these approaches, and devise some ethics to deal with them. In our vanity, we imagine that we control these sources. But the truth is that they are very deliberately seeking to control us.

The second intelligence tactic of manipulation which gives concern is the habit of allowing spies to write under false names. It was Tomlinson, I suspect, who, having worked in the area, first blew the whistle on this one. And it was a recently published book - MI6 by Stephen Dorril - which once again added the final piece of the jigsaw.

Two articles appeared in the Spectator in early 1994 under the byline Kenneth Roberts. They were datelined Sarajevo, and Roberts was described as having been working with the UN in Bosnia as an adviser. In fact, he was MI6 officer Keith Robert Craig (the pseudonym was a simple one), whose local cover was as a civilian "attached" to the British military unit's Balkan secretariat.

At the time, Bosnia was the site of attacks and atrocities from neighbouring Serbia, and also the focus of some passionate reporting from British journalists. The British military was there in a UN peacekeeping role, but anyone who read Roberts's articles might have begun to wonder whether it was not a better policy for British troops to go home and leave the Serbs a free hand.

The first article on February 5 rehearsed arguments for a UN withdrawal, pointing out that all sides committed atrocities. The second piece complained, baselessly, about "warped" and inaccurate reporting by journalists, including the BBC's Kate Adie.

It is possible, of course, that Craig was merely overcome with private literary urges whilst marooned in the Balkans, and thought it more politic to express his own opinions under a nom de plume . But one of the traditional roles of I/Ops is to plant stories. What is not clear is how the introduction to the Spectator was made, or whether Craig confided his real trade to the then editor of the Spectator, Dominic Lawson. In his recent book about MI6, Stephen Dorril points out that Dominic Lawson's brother-in-law, Anthony Monckton, was himself a serving MI6 officer, who was to take over the Zagreb station in the Balkans in 1996. (Rosa Monckton, his sister and Dominic Lawson's wife, was the late Princess Diana's close friend.)

These relationships - which the disenchanted Tomlinson knew all about because he had himself served undercover in the Balkans in the same time-frame - have only slowly emerged into the public domain. There is no reason to believe the then editor of the Spectator did anything improper at all, and certainly no reason to think that he was acting as an agent of MI6, whether paid or unpaid. But, as an editor, wittingly or not, it must be a bad idea to end up in a position where an MI6 officer is writing for your publication on matters of political controversy, under a false name.

The final malpractice which the Tomlinson/Shayler defections have brought to light is the continuing deliberate blurring by MI6 of the line between journalist and spy. This is an old crime - Kim Philby, former foreign correspondent of the Observer would have had plenty of stories to tell about that. But it should be exposed and stopped. Tomlinson himself, by his own account, spent six months in 1993 travelling around Croatia and Serbia trying to recruit informants, under the guise of a British journalist. Dorril, in his book, publishes the further assertion that the Spectator itself was unknowingly used as cover by no fewer than three MI6 officers working in Bosnia, Belgrade and Moldova.

The most dismaying allegation floated by Tomlinson was that he had heard within MI6 of a "national newspaper editor" who was used as an agent, and had received up to £100,000 in covert payments, accessed at an offshore bank, via a false passport obligingly supplied by MI6 itself. This claim set off a hue and cry, during which the hapless Dominic Lawson, now editor of the Sunday Telegraph, issued his denial, and other editors came under suspicious scrutiny.

In fact, I believe Tomlinson has been wrongly reported. Those who have talked to him in detail say that he has no first-hand knowledge, but merely knew of something a colleague obliquely mentioned. Hearing the words "editor" and "national newspaper", Tomlinson jumped to the wrong conclusion, and then started guessing. Spies are, after all, very like journalists in their methods - but merely less reliable. What those in the newspaper business know is that there is all the difference in the world between "the editor" and "an editor". Newspapers have, for example, education editors, environment editors and defence editors (not, I should say, that I have any evidence against any individual members of these categories).

And a senior journalist at that level - who could travel, see things, report back - would be of more practical use in the business of espionage than, say, the editor of any national newspaper. So the hunt is still on for the miscreant. And, make no mistake, this kind of behaviour by journalists is dangerous and wrong.

Our first task as practitioners is to document what goes on in this very furtive field. Our second task ought to be to hold an open debate on what the proper relations between the intelligence agencies and the media ought to be. And our final task must then be to find ways of actually behaving more sensibly.