Of all the politicians to be hoodwinked by the securocrats, an unlikely figure is the cigar-chomping, cricket-watching Ken Clarke. But beneath the veneer of consultation and compromise, the Justice Secretary – otherwise known as the liberals' extra man in Cabinet – is seeking to introduce changes to Britain's justice system that challenge the very heart of a fair trial.

The Justice and Security Bill, in its present just as in its previous form, is a bad Bill. For sure, it could be worse; indeed, it was worse. Improvements have been made during many hours of arduous Coalition horse-trading involving Nick Clegg, his team, the Ministry of Justice, Foreign Office, Home Office and, of course, the spooks.

Definitions have been narrowed. The role of judges has been clarified. But, if the Bill makes it to law roughly in its present shape, the security services will have greater jurisdiction than ever before to withhold information from court that casts them in a bad light.

The impetus for the Bill results from the case of Binyam Mohamed, who, in February 2010, won his case in the Court of Appeal over the collusion of MI5 and MI6 in his torture. Whitehall did everything it could to suppress an earlier High Court judgment which condemned the UK for its "cruel, inhuman and degrading" behaviour towards Binyam Mohamed. This was a classic case of an inconvenient truth and the extent to which those with power seek to suppress it for their own interests. With cases pending about the role of the British in the illegal rendition of Libyan dissidents into the hands of Colonel Gaddafi's secret police, it is hardly surprising that everything is being done to try to keep these sordid activities away from the public domain.

Another aspect of the Bill is the extension of what is known as closed material proceedings, whereby evidence deemed harmful to "national security" is heard in secret. In trumpeting his propensity to listen and learn, Clarke yesterday pointed to the fact that judges, rather than ministers, will make that call.

He also suggested that the term "national security" was an agreeably narrow interpretation, although, as any lawyer will attest, that covers a multitude of sins. The original plan was to give ministers blanket authority to impose secrecy on any relevant civil case whose disclosure might be "harmful to the public interest". The Bill does presage one improvement. In future, parliament's Security and Intelligence Committee will have greater say in the appointment of its members.

The Bill, in its original form, was strongly and unanimously criticised by parliament's joint committee on human rights. So ministers decided to act. This follows a well-trodden path in policy-making: publish a draft Bill that is so egregiously extreme, make a certain number of concessions (usually during the legislative process but, in this case, earlier on), and everyone ends up happy with the so-called compromise.

The Conservatives and other hardliners emerge with their Bill relatively intact. The Liberal Democrats proclaim the work that has been done to improve matters. Both assertions are true. (It will, incidentally, be interesting to see whether Labour's long-standing and increasing disdain for issues of judicial rights will lead to support for the Bill, tempered by criticism of government "incompetence". So far, there is little evidence to suggest that Yvette Cooper, the shadow Home Secretary, has learnt from the woeful tenures of David Blunkett, John Reid and Jacqui Smith.)

While the politics of the Turkish carpet bazaar might work for some aspects of policy, in areas of justice and civil liberties, it is inappropriate and dangerous. One assumes that the otherwise laudable Clarke, in his twilight political years, thought this was a battle not worth fighting. He admitted last month that the Government was acting largely at the behest of the Americans, who he said "have got nervous that we're going to start revealing some of their information". As a result, they had started to cut back on intelligence sharing. That much is apparently true – and worrying.

The Americans bear down on the Brits because they know they will get away with it. They did so in order to secure an extradition treaty that is woefully one-sided. They do so in other areas of security and intelligence, and diplomacy. And who can blame them?

There may well have been the need for certain tweaks to be made around the admissibility of certain sensitive evidence. But there is already a procedure, known as public interest immunity certificates, that allows the prosecution to apply for a restraint on disclosure. These gagging orders are already strong.

Underlying these often-technical discussions is the fundamental and perennial question about the balance between security and liberty. As many former ministers attest, it takes some doing to face down the spooks who, closing the door behind them, tell you to be scared, very scared. Most succumb all too easily. Once more, it falls to unelected peers of the realm and, after them, the judges, to assume the role of guarantors of liberties that many elected politicians gave up on long ago.

John Kampfner is the author of 'Blair's Wars' and 'Freedom For Sale'

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