Tensions between ministers and the judiciary have become a hallmark of this Government to the point where we sometimes seem close to replicating the American system of institutional checks and balances. But the fracas that has broken out between the politicians and the judges over the sentencing of a recidivist paedophile, Craig Sweeney, has served to bring a host of long-simmering disputes to a head.

The trial judge sentenced Sweeney to a minimum term of five years' imprisonment. The Home Secretary, John Reid, echoed an outcry in the popular press by calling the sentence "unduly lenient" and publicly asked the Attorney General, Lord Goldsmith, to re-examine it. Lord Goldsmith made known his unhappiness at the request. The Prime Minister, through his spokesman, supported Mr Reid's right to "articulate the concern the public has" and repeated his determination to "rebalance" the judicial system in favour of victims.

Enter the Lord Chancellor, Lord Falconer. In a BBC interview, the country's highest-ranking judicial official and former flat-mate of the Prime Minister came out squarely on the side of the judiciary. Yes, he said, he believed the sentence was too low. But no, it was not the fault of the judge. "I believe it was the fault of the system."

Several interpretations can be placed on the Lord Chancellor's words. In one, he would be placing allegiance to clan, the top judges, ahead of loyalty to the Government. In another, he would be preparing his own smooth transition into the post-Blair era. And there may be an element of truth to both. But the simplest explanation is that the Lord Chancellor accepts - quite rightly, in our view, and not before time - that ministers' efforts to limit the discretion of judges have gone too far.

The unhappy truth is that the judge in the Sweeney case was only following government guidelines when he set five years as the minimum Sweeney would spend in prison. It was his bad luck to be hearing a highly emotive case in which the accused could theoretically qualify for every discount on offer. The supposed five-year sentence was a gift to the law-and-order lobby, as the Home Secretary and the Prime Minister understood at once. It also fed into a stream of reports about judicial and Home Office laxity, according to which dangerous felons were released early, left unmonitored by a hopelessly inadequate parole system and almost invited to reoffend.

In fact, the sentence in this case was not as lenient as its multitude of critics chose to suggest. It is highly unlikely Sweeney will ever qualify for parole and he could be in prison almost indefinitely. But five years was the minimum sentence, calculated according to fixed formulae, and inevitably, it was this, not the maximum, that made the headlines in a popular press leading a hue and cry against a judiciary it regards as too liberal and a Government it sees as "soft" on crime.

That the outcome of this case could be "spun" in this way, however, is largely, if not entirely, the Government's own fault. New Labour campaigned as a party that would be tough - as tough as the Conservatives - on crime. In office, it has tried to tie the hands of judges it has seen as resistant to its hard line on terrorism and national security. Faced with burgeoning costs and overflowing prisons, however, it has encouraged discounts for guilty pleas and good behaviour, without developing a parole system to match.

Any confusion here is of the Government's own making. It has run scared of the popular press and talked a tougher game than it was prepared to play. Not for the first time, and probably not for the last, it has been hoist by its own presentational petard.