The BSE report has highlighted the disastrous consequences of the age-old battle between government and the Civil Service

Anticipating a high-voltage political event, most cabinet ministers cleared their diaries last Thursday morning. They wanted to be in the Commons to hear the Minister of Agriculture, Nick Brown, make his statement on the BSE report. Already the newspapers had been full of dramatic stories about how the report targeted ministers and officials from the last Conservative government.

Anticipating a high-voltage political event, most cabinet ministers cleared their diaries last Thursday morning. They wanted to be in the Commons to hear the Minister of Agriculture, Nick Brown, make his statement on the BSE report. Already the newspapers had been full of dramatic stories about how the report targeted ministers and officials from the last Conservative government.

But the exchanges in the Commons were dry. As political theatre it was a huge anticlimax. During Mr Brown's own wooden speech, a minister sitting near by whispered to another colleague: "This statement has been written by the bloody Civil Service."

When he left the chamber, the minister reflected further. Here was a highly emotive issue with devastating political implications, but Mr Brown sounded as if he had been reading the football results. "The officials neutered the statement. They can't write in proper English. They failed to make any political points about the last government being culpable. I make sure I write my statements myself."

Here is an emblematic double whammy. While Mr Brown was summarising a report that is highly critical of Whitehall's performance over BSE in the mid-1990s, a minister was expressing his irritation with the current performance of civil servants. He is by no means alone. According to one former senior official who remains in contact with civil servants at the highest level: "There is now a colossal stand-off between the Government and Whitehall that is potentially very destructive."

From the perspective of some ministers and their advisers, the stand-off will be resolved only when the culture in Whitehall is transformed. The BSE report is their latest, most potent ammunition. "The BSE report confirms everything we have been saying about Whitehall as a whole," says an adviser appointed by a senior Blairite minister. "Whenever there is a potential conflict between different departments, or an awkward problem, they do not search for the right answers. Their priority is to defend their own departmental position. They do not share knowledge, but keep information to themselves. They judge the quality of their work purely on the basis of how well they defend their own department."

The most commonly expressed complaint is that everything happens so slowly. "Most civil servants," says one minister who has worked in two of the biggest government departments, "are not interested in delivery. They like to be involved in policy-making, but delivery and measuring the success of the policies are seen to be lower-grade activities."

According to Tony Blair, last year was supposed to have been "the year of delivery". There were not many signs of policies being delivered on the ground. Civil servants are getting some of the blame. "For the top 3,000 civil servants," says one influential adviser, "policy development is all that matters. Implementation of policy is for the second-raters. If you fail as a policy-maker, you are sent to a regional office responsible for delivery."

Another appointed adviser puts it more vividly: "Those civil servants who are sent to the social security offices in Newcastle and Glasgow are regarded like the not-very-bright young sons of families in Victorian England who were sent off to run a sheep farm in Australia."

Ministers glance enviously at the three departments that have to some extent transcended what they see as Whitehall inertia: Downing Street itself, the Treasury and the Department for Employment and Education. "Tony," says one insider, "doesn't realise quite how bad it is in the rest of Whitehall because he brought his own people in and has the pick of the best civil servants. Gordon [Brown] and David [Blunkett] also brought in people with whom they worked closely in opposition. They have taken on the machine and won."

Blunkett's department has seen something of a revolution. The Permanent Secretary, Sir Michael Bichard, was appointed from the outside after a long career in local government. He has tried to break the parochial Whitehall traditions by bringing in senior teachers and education specialists when policies are being developed in the department. His officials have been far from thrilled at this innovation. Bichard met with even greater resistance at a Sunningdale conference earlier this year when he proposed that potential high-fliers should spend two or three years in service delivery. This led to a minor rebellion among his fellow senior officials. In the end they agreed, with some reluctance, to phase in the proposal over several years. Some ministers fear it will be decades before it actually happens.

In this increasingly bitter conflict, officials are starting to put their case more forcefully. Robert Hazell, the director of the Constitution Unit at University College London, was a senior civil servant for 14 years. As his unit has been a pioneer of constitutional reform for several years, no one can accuse him of being a conservative on these matters. Yet Hazell believes that ministers have gone too far in their hostility to Whitehall. "Ministers are relying more and more on their advisers, and leaving civil servants out of the loop. This leaves civil servants in the dark as to what ministers really want, and in some departments it slows things up because these advisers become an acute bottleneck." In other words, when ministers complain about delays, they themselves are often to blame.

Ministerial impatience is also often misplaced, according to a senior official from one of the bigger departments, who suffered similar outbursts of anger under Tory administrations. "Ministers ... think when they've announced a new initiative that it's happened. But it can take years to implement a new policy ... it's the job of the Civil Service to ensure proper procedures are followed: fair and open competition, no favouritism, no short cuts. That all takes time."

Even so, armed with the BSE report, senior Blairites are pressing for further reform. "We have to break down barriers between the departments - that's the main message of the report," they say. Mr Blair has made one substantial innovation with the introduction of the Social Exclusion Unit, where officials and ministers from several departments meet regularly. If Labour wins a second term it is expected that he will go much further.

One Downing Street insider expects to see the establishment of far more project teams, bringing together officials from up to eight departments to form permanent teams for several months, or longer if necessary. He gives the example of tackling poverty for lone parents.

In spite of the tensions, there are areas of agreement. Both ministers and senior officials say more must be done to recruit outsiders, especially more women and people from ethnic minorities. Ministerial modernisers also acknowledge that there are no models outside Britain which are any better. Some Blairites have looked for inspiration towards the US, Canada and even New Zealand, but the political systems are so different that they offer little guidance for reform.

Even so, there is a rare opportunity hidden in the growing tensions between ministers and officials. After 18 years of Labour opposition, ministers have a clearer sense of the real world than officials who have spent their lives in an intoxicating Whitehall hierarchy. On the other side, there is some sensitivity from Blairites and their advisers about the charge that they are control freaks. The BSE report will now be placed into this melting pot. If the Civil Service does not reform itself now, it probably never will.