A frightfully uncivil service

He hadn't written a resignation letter. It didn't come to that. But Stephen Byers knew as he walked into the Commons chamber that within an hour his "fate would be sealed one way or the other".

And so the beleaguered Transport Secretary strode up to the dispatch box and gave the performance of his life, apparently untroubled that in saving his own career and reputation, he sacrificed those of two senior civil servants – Martin Sixsmith and Sir Richard Mottram.

In doing so, the Secretary of State for Transport exposed the dysfunctional relationships between the minister, his political aides and the civil servants in his department.

Since 11 September when his special adviser Jo Moore sent her now infamous email, Mr Byers had been presiding over a department at war. Between then and the fatal email, warning Ms Moore against releasing rail statistics on the day of Princess Margaret's funeral, briefings against colleagues became the norm at the Department of Transport, Local Government and the Regions.

With almost clockwork regularity, the private business of the department was becoming public knowledge. When one of Ms Moore's friends was in line for a top job in the press office, the story of her involvement – whether true or not – found its way into the press. When the Heathrow Airport Terminal 5 decision was due to be announced, tales of the black art of spin accompanied every report.

The growing civil service resentment of Ms Moore was unbearable. Inevitably, something had to give.

Who was responsible? Someone in the department. But perhaps not the person who paid for it in the end.

What seemed to suit both politicians and senior civil servants was to maintain that the problem in the department was an isolated case and the clash between Jo Moore, the special adviser, and Martin Sixsmith, the civil service director of communications, was a one-off.

"It's been pretty awful in there," a source at the First Division Association, the civil service union, said. A Whitehall source said: "Morale has been hit pretty badly in there. The atmosphere is horrendous. I mean, how would you like it if every time you turned on the television someone was slagging off the place you worked?

"They all feel as if they've been tainted by what's gone on. And they're scared. They're scared that they might be next."

The First Division Association stresses the DTLR is "unique" in this respect. But there is an admission that relationships right across Whitehall now need to be rebuilt.

Five years ago, civil servants clapped and cheered as New Labour swept into office. Relations soon soured. The Yes, Minister culture of a civil service trained to run the country while letting ministers believe that was what they were doing riled the ambitious politicians and their loyal special advisers who'd sweat blood to get them elected.

One said last week: "Rolls-Royce civil service? What a load of crap." The remark betrays the frustration felt by many on the political side of the fence. Another special adviser said: "The Civil Service just aren't geared up for delivery. And that's what we need them to be."

Worse is the suspicion that some in the Civil Service are not merely "incapable of doing the job" but are "deliberately obstructive".

"These people are not impartial civil servants. Whether they know it or not they are conservatives either with a big C or a small c and they are trying to undermine the Government," a political source said.

Ministers have lobbied hard for the Civil Service to be reformed, for new life to be breathed into what they soon came to see after 1997 as an archaic machine.

One said: "There was a move to sharpen up various departments. There was very much a Yes, Minister approach where ministers were given all the options when it was clear that in the mind of the civil servant it was actually a fait accompli. Some of them would just direct us into what they wanted to see. Eighty per cent was what the Civil Service wanted. It was all incredibly frustrating."

It became more than frustrating and was soon seen as "undemocratic". A Labour adviser said: "We live in a democracy where people vote for a political party; they get elected and form a government to implement the programme on which they were elected. The Civil Service is there to serve the ministers the people have elected.

"It's about who runs the country. It's about time the Civil Service stopped thinking it was them."

The phenomenon is by no means new. A former Tory minister recalled difficulties in the immediate aftermath of the 1992 election, one the Tories were expected to lose.

He said: "There is a supertanker effect. It's particularly difficult for some ministers if you want to do something they don't or don't want to do something they do. The Civil Service could get quite antagonistic and sometimes menacing. They could be uncooperative and even obstructive."

The real problem then seems to lie not in the party political leanings of individual civil servants but the nature of the Civil Service itself. One civil servant said: "The whole raison d'être of a civil servant is to avoid cock-ups. Why do you get promoted in the Civil Service ? Because you don't make mistakes. Inevitably, we conduct ourselves with caution."

Both sides stress that things are not all bad. There is a suggestion that special advisers should be trained like civil servants. On the other side of the fence, there is a counter-suggestion that civil servants should be trained like Millbank apparatchiks.

The third option seems to be to get on with it and skate over the underlying tensions – in essence, the status quo.

As far as the Civil Service is concerned, the onus is on ministers – who, despite mutual respect in some departments, some senior civil servants see as "image obsessed", "addicted to unworkable policies" or "prone to blaming anyone but themselves".

"There is a responsibility on ministers to recognise the importance of building relationships," an FDA source said. "Some of the remarks being made by ministers are unhelpful. And everybody has to work together to make sure this doesn't turn into a huge stand-up row."

There is a functioning relationship in some departments where individual ministers and their aides have worked hard to win the respect of the civil servants. Elsewhere, the civil servants complain, they have simply been elbowed out of the way in favour of party appointees. Downing Street and the Treasury, they argue, are effectively run by a new breed of "political civil servants".

But elected governments and the Civil Service are the archetypal warring couple: they can't live with each other and they can't live without each other. Some might say they deserve each other.