So why didn't the police go for David Davis? This is one of the questions hanging in the air after the arrests of the Tory immigration spokesman, Damian Green, and Christopher Galley, his Home Office source. After all, Davis was Green's boss when Galley first made contact in 2006. The former shadow home secretary and Tory leadership candidate has written: "Damian is among the most straightforward and honourable of people. He worked for me when I was shadow home secretary. Everything he did as shadow immigration minister he did with my implicit or explicit support." Is it conceivable that Galley made direct contact with Green? Far more likely that he would have approached tough-talking Davis, who had a long-standing reputation as a ministerial scalp-taker and had already made use of leaked information to embarrass Beverley Hughes and David Blunkett. Peter Mandelson is almost certainly right when he suggests such a sensitive whistleblower relationship would have been cleared at the highest level of the Conservative Party, possibly by David Cameron himself.

At the time of writing, Davis had not been questioned by the police, though they are said to be interested in what the MP for Haltemprice and Howden might have to say. But the Metropolitan Police is in difficulty here. If officers invite Davis for a polite chat it will be hard to explain why this approach was not used with Galley and Green. The police have displayed a grave (if understandable) failure to grasp how politics works. This, rather than a political decision to target a member of the opposition, is likely to have been behind the raid on Green's offices. The Home Secretary, Jacqui Smith, has talked repeatedly of the importance of respecting the "operational independence" of the police, but there is a clear conflict when this interferes with the operational independence of a member of parliament.

The shadow immigration spokesman is an unlikely martyr. A former president of the Oxford Union with a reputation while a student as something of a Tory "wet", he has done nothing more radical in his life than support Davis in the 2006 leadership election. Even then, he was backing the favourite. A former party official who knows him well said: "He drives a Volvo, for God's sake. He wears Marks & Spencer suits which are shiny at the arse and the elbows." Tory sources suggest Green was given the Home Office mole to "handle", much as an intelligence officer would be given an agent to run by someone further up the hierarchy.

MPs and commentators have been rightly appalled at the treatment of Green, who is said to be particularly furious that his child's bedroom was searched by police. There is also concern, which stretches to cabinet level, about the way officers of the Met were allowed to enter the precincts of parliament to search Green's office. Jacqui Smith and Gordon Brown have emphasised the importance of MPs not being seen to be above the law. The inquiry by Ian Johnston, head of British Transport Police, will have to examine whether the response was proportionate, considering the nature of the alleged crimes.

Several questions remain unanswered in this most singular of cases. Why was the Home Office so exercised by such minor disclosures? They were good scoops for the right-wing press, but by no means huge breaches of national security. Indeed, the arrests were not made under the Official Secrets Act. The police would certainly have used the OSA if they could, because its terms are sweeping and offer no room for a public-interest defence.

It is worth looking at the stories that emerged from this allegedly criminal relationship. The first revealed details of Home Secretary Smith's attempts in July 2007 to manage the story that thousands of illegal immigrants had been allowed to work in security-related posts. Ultimately Smith was forced to admit that as many as 11,000 illegal immigrants had been cleared by the Security Industry Authority. The second involved a memo to the Home Office minister Liam Byrne in January 2008, admitting that an illegal immigrant had been employed as a cleaner at the House of Commons. In August, a third leak revealed that Smith had written a draft letter to Downing Street warning that the economic downturn might lead to a rise in crime. In addition, names of Labour MPs likely to rebel against the proposal to extend detention without trial to 42 days for terror suspects may also have been leaked.

Can the government argue the release of such information was damaging to anything except its own reputation for competence? Could this information not have been placed in the public domain? Ministers themselves concede the draft letter to Downing Street, for example, only stated the obvious.

A genuine worry for ministers is that the slow drip-feed of confidential information to the opposition or the press makes the work of government impossible. Ministers and civil servants need to know that their deliberations will go no further than the walls of their offices. But this risk is hugely overstated. Considering its size and the number of controversial decisions made daily, Whitehall is remarkably unleaky.

This was a point once made forcibly to me by America's most famous whistleblower, Daniel Ellsberg: "You journalists naively believe 'the truth will out'. You don't know the half of it. In fact, you know less than a fraction of 1 per cent. Almost nothing leaks." Thus the man who leaked the Pentagon Papers, a detailed history of America's involvement in Vietnam from 1945-67, enlightened me to a harsh reality: most government secrets remain secret. Even the best-informed journalists just scratch the surface of what is going on. It is often not necessarily the most important and almost never the most outrageous acts of government that are leaked.

The publication of the Pentagon Papers in 1971 by the New York Times wholly undermined the US government's case for war. Christopher Galley is no Daniel Ellsberg, but he says he acted from the same principle: a government was attempting to hide information that should be in the public domain.

Green's arrest and the breach of the conventions of parliamentary privilege that the search of his office entailed are shocking events. Yet something positive may come from this. As a serial disseminator of leaked information myself, it has been my experience that the authorities tend to go for the weakest individual in the chain of disclosure. This is occasionally the journalist, but more often the "mole". This government has a record of shooting the messenger.

In the two high-profile cases I have been involved with, the GCHQ whistleblower Katharine Gun and the Foreign Office mole Derek Pasquill, the individuals had their lives held in suspension for months while waiting to be charged. Both lost their jobs. The mental toll of fighting the government can be heavy, as the former MI5 officer David Shayler discovered. Finding work afterwards is very difficult. At least, with the arrest of a senior politician, we can have a full discussion in parliament about the uses and abuses of government secrecy.

The Green case will have implications for government and for journalists. There are MPs across Westminster to whom I have shown leaked documents - including one leader of an opposition party. How else would they be able to judge whether it was appropriate to discuss their contents under the protection of parliamentary privilege? I will think twice about showing them such material in future and I am sure they will be wary of handling it. As it turns out, I have more protection under the Police and Criminal Evidence Act from disclosing my files as a journalist than MPs derive from convention laid down over the centuries.

The government has oscillated between attacking the Tories for condoning alleged criminal activity and recognising that MPs are worried about the implications of allowing police officers into parliament. But when the dust clears, people should take a long look at the alleged offence for which Green and Galley were arrested. According to the law manuals, the offence of misfeasance in public office is designed to target the "deliberate and dishonest abuse of power". In effect, this criminalises a relationship that has always existed between opposition politicians and their government sources. The government must tread carefully, because for most people looking at the extraordinary events of recent days Damian Green was the victim, not the perpetrator, of an abuse of power.