It cannot be long before Damian Green is nicknamed the “Memo Martyr”. After his arrest last week over leaked Home Office documents, the Conservative frontbencher has become a champion of liberty, a hero of constitutional proprieties, a figurehead for parliamentary independence.

He has a right to be outraged by how he was questioned by police for nine hours as punishment for doing his job. He is justified in being angry at how officers rifled through love letters to his wife in his constituency home. The raid on his Commons office was a breach of parliamentary privilege - and in a press conference yesterday, a solicitor for his alleged source, Chris Galley, made clear that the Home Office did not believe he was being “groomed” to betray his employer. “There is a general acceptance that the whole thing has been too heavy-handed,” one minister said yesterday.

But this case is not just about the constitutional role of the Opposition. It also reveals a more general concern at the highest level in the Civil Service about how the workings of government are being revealed. As interesting as the questions about the behaviour of the police towards Mr Green is why the Permanent Secretary at the Home Office, Sir David Normington, and his boss, the Cabinet Secretary, Sir Gus O'Donnell, decided to set the boys in blue on the boy in blue.

The truth is that the Shadow Immigration Minister was the victim of this sting - but the real target was much wider. There is a growing frustration in Whitehall that the Government is losing control of the very thing on which its power depends - information.

This is the Government that introduced the Freedom of Information Act, yet it is drowning under the weight of democracy in action. It's not just about leaks - although some believe there is also a Civil Service mole in the Treasury, after the early publication of parts of the Pre-Budget Report.

In the view of the mandarins there is a more systemic problem. The Freedom of Information Act, designed to open up the workings of the political elite to the masses, has, they believe, turned into a huge distraction. Last week, the Cabinet Secretary made clear his irritation when he gave evidence to a tribunal considering whether the minutes of Cabinet meetings in the run-up to the war in Iraq should be released. Other senior civil servants moan about the time they spend on freedom of information requests. “The whole thing has become a nightmare,” says one permanent secretary. “It is starting to hamper the way in which Government works.”

They have a point. Of course, as a journalist I am all in favour of getting as much information as possible. But there comes a time when the public interest means that some things should be kept private. If the Information Commissioner decides that the details of Cabinet meetings should be released it will become almost impossible for ministers to have a frank discussion.

Officials have already become more circumspect in the advice they give for fear that their private musings will be released. People are reluctant to put things on paper. Even in e-mails civil servants use codenames, or replace some letters with asterisks when discussing individuals - so that a search for the person's name under the Freedom of Information Act, would draw a blank. Legislation that was meant to encourage more openness has, in fact, led to greater obfuscation. Sir Gus jokes with investigative journalists at parties that it is his job to frustrate their inquiries; the Civil Service sees its role as to block any important requests, which means that only trivia (such as the guest lists for dinners at Chequers or the amount of money MPs claim on expenses) is revealed. “Most ministers think that the Freedom of Information Act is a joke and a waste of taxpayers' money,” says one government member. “It's killing the system.”

There were 8,865 freedom of information requests in the past three months for which records are held. Hundreds of civil servants have to work full-time on answering the questions, at a cost of more than £20 million a year. Officials estimate that they have spent more than £1 million answering requests from the BBC alone. Lord Turnbull, Sir Gus's predecessor as head of the Civil Service, once told me he had to devote an hour a day to deciding which documents should be made public while a minister claims he spends twelve hours a week answering “scrutiny” questions including those submitted under the Freedom of Information Act. Many requests are a waste of time - one questioner asked how much money was spent on Ferrero Rocher chocolates by British embassies; another woman asked for a list of phone numbers of eligible bachelors in the Hampshire police force. Legislation designed to increase voters' trust of the political system has ended up undermining it.

A related problem is the rise in the number of political memoirs. Ministers have always set out their side of the story, after retiring - but what is new is the speed of publication, and the decision by advisers such as Alastair Campbell to publish their almost instant thoughts. The 30-year rule has become the 30-day rule. Confidences are betrayed, details of private meetings leaked, former colleagues trashed in return for a sufficiently large advance. At the same time, politicians still in office pretend to be more open than they are. They have blogs, Twitter updates and Facebook profiles - but reveal nothing of real interest. It is a mismatch that just further undermines voters' respect.

Mr Green has touched a nerve in Whitehall. But what is needed is a proper discussion about the limits of what the Government should be expected to reveal. Trying to control the flow of information, in the internet age, is like attempting to handcuff a jelly. The solution is not to handcuff a member of Her Majesty's Opposition.

Times Recommends

• Strip away the figleaf and reveal naysayers
• Dave’n’George: there may be trouble ahead
• I do not accept that £64,000 a year for politicians is peanuts