Andrew Grice: He meant to open fire on the Tories. Instead, Brown shot his own troops

The floor of Gordon Brown's room at the House of Commons was plastered with the parliamentary expenses claims made by his ministers. Remarkably, the exasperated Prime Minister was ploughing through reams of paper by himself, to find out which MPs it would be safe to promote in an imminent reshuffle.

The incident, which happened just before his cabinet shake-up in June, highlights both Mr Brown's inability to delegate and just how much the controversy over MPs' expenses has cast a shadow over British politics since it broke in May.

After a brief summer respite, the cloud returned this week. For Labour, it was supposed to be the moment to turn its guns on the Tories after the party conference season. Instead, many Labour MPs feel that Mr Brown declared war on them, by ordering them to meet the payback demands of Sir Thomas Legg, the former Whitehall mandarin called in by the Prime Minister to audit all MPs' expenses claims from the past five years.

"Gordon has turned us into criminals," one Labour MP said. It was not untypical. Feelings are running high. For some Labour MPs, Mr Brown's handling of expenses might even be the "tipping point" as they decide whether to join yet another looming rebellion aimed at ousting him before the general election.

Even Brown allies acknowledge that Sir Thomas, desperate to avoid allegations of a whitewash, has exceeded his brief by imposing retrospective annual limits on what MPs should have claimed – such as £1,000 for gardening and £2,000 for cleaning.

MPs in all parties are seething. Not only did Commons officials approve the money they must now repay; in many cases, they were actively encouraged by officials to claim it under headings now deemed inappropriate.

Their anger is real and understandable. Seen from the Westminster village, the Legg approach is extremely unfair. Ironically, it has been unfair on Mr Brown personally. He was quick to repay more than £12,000 for cleaning and gardening after falling foul of the retrospective limits. Brown allies are seething that he gets bad headlines about his relatively modest claims, while David Cameron collects good ones about cracking down on Tory MPs and – so far – escapes personal criticism, even though Labour claims that he played the system. The Tory leader took out a £350,000 mortgage on his Oxfordshire house, close to the maximum amount for which interest could be claimed under the "second homes" allowance, and four months later paid off the outstanding £75,000 loan on his London home. There is no suggestion he broke Commons rules.

Despite the talk of revolts, legal action or voting down the Legg proposal in the Commons, party leaders and more sensible backbenchers realise that MPs have got to swallow the horrible medicine because of the view in the real world. "People won't understand if we fight this; £24,000 [the maximum annual 'second homes' payment] is more than the average annual wage in my constituency," noted one Labour MP.

That is why, in May, Mr Brown judged that a new expenses system for future claims would not be enough; the public would be re-assured only by an independent audit of past claims too.

It may have taken a while for the penny to drop for Mr Brown, but once it did, he went at the expenses issue with guns blazing. "The MPs don't get it," he told a close ally shortly before announcing his proposals. "Self-regulation [by MPs] is over. The public won't wear it. There has to be transparency. We have got to clean it up."

The Prime Minister believed he had to give a lead to save Labour MPs from themselves – and possibly save their seats. "He saw an oncoming train that was going to flatten them," one aide recalled yesterday.

Not for the first time, Mr Brown made the right call on a big issue and then made a mess of implementing it. He didn't consult Labour MPs or opposition party leaders before pre-empting a review of expenses by the Committee on Standards in Public Life by rushing out interim changes. That allowed MPs in all parties to defeat his proposal to replace the "second homes" payment with a daily Commons attendance allowance. He also made a hash of announcing his plans in his "smiley" YouTube video.

Nor did Mr Brown take his Cabinet with him. Some ministers now complain, perhaps with hindsight, that the Legg review was unnecessary, that the Prime Minister has created a monster that will be on the rampage until the new year, wasting precious pre-election time and eclipsing Labour's attempts to highlight the choice between the two main parties.

There is tension between Mr Brown and Harriet Harman, who is responsible for expenses as Leader of the Commons. She is said to feel she could have spotted some of the elephant traps if only Mr Brown had kept her in the loop. He is said to be less than enamoured with her handling of the detail. And Brownites suspect she is playing to the Labour gallery by saying that the Legg review cannot be "arbitrary", a different line to Mr Brown's payback demand.

Perhaps we will look back on the expenses saga as a symbol of the Brown premiership: nine out of 10 for the decision, three out of 10 for delivering it. When Mr Brown "gets it", he expects everyone else to instantly, doesn't take people with him, gets impatient, bulldozes ahead and crashes. So even when he's right, it goes wrong.

Mr Brown, Mr Cameron, Nick Clegg and the Commons Speaker, John Bercow, are right to say it's payback time. To unpick the Legg recommendations would defeat the object of an independent inquiry, sending a terrible signal to the voters and further undermining trust in the political system. Yes, for many MPs it is unfair. Life is. Many of their own constituents could have told them that.