Brown faces a furious backlash from MPs told to repay expenses

More than 300 MPs will today be asked to pay part of their expenses or produce evidence to back up old claims.

Politicians will return to Westminster this morning – after an 82-day summer recess – to scenes of anger and recrimination, as all 646 MPs receive individual letters from Sir Thomas Legg, the retired civil servant called in to carry out an audit of MPs' expenses, going back five years.

Gordon Brown will face a furious backlash from MPs, including from within his own party, who say they are being punished over their expenses claims when they did only what the rules allowed them to do at the time. The timing has dashed the Prime Minister's hopes that he could use Parliament's first day back after the summer break to begin a fightback against the Conservatives over economic policy.

Instead, he will return to a Commons seething with rage over Sir Thomas's inquiry, and with some Labour MPs still hoping that they can organise a coup to remove Mr Brown from office before the election. This evening, the Prime Minister will face the weekly meeting of Labour MPs and peers, where protests are expected about the scale of the Legg inquiry.

Yesterday, Downing Street defended the decision to call in Sir Thomas. Mr Brown himself is expecting a letter today calling on him to repay part of the £6,577 he claimed for cleaning bills for his London flat. The money was paid to his brother, Andrew, who arranged to have the flat cleaned.

The hundreds of other MPs likely to be caught in Sir Thomas's net include many who "flipped" from one second home to another to make the most of the £24,222 second-home allowance, a practice that was permitted at the time but is now banned.

The Chancellor, Alistair Darling, flipped four times in four years on three different properties. Geoff Hoon, who resigned from the Cabinet in June during a reshuffle, flipped his second home and did not pay capital gains tax on the sale of London property.

The Tory MP Sir Patrick Cormack is expected to be asked to repay thousands of pounds from the £11,212 he claimed in four years for cleaning his Westminster flat. The Labour MP Bob Marshall-Andrews claimed £118,000 over seven years for second-homes expenses, including stereo equipment and Kenyan carpets.

Alan Johnson, the Home Secretary, described the Legg inquiry as "the solution not the problem". But other MPs have protested that Sir Thomas, a 74-year-old barrister with a long civil service career, has gone much wider than his original terms of reference.

Sir Stuart Bell, a member of the Commons Members Estimate Committee (MEC), which is overseeing the Legg inquiry, forecast yesterday that aggrieved MPs "will have in their breast pockets a letter from Sir Thomas, dated 2 July, saying that this review would be carried out in accordance with the rules at the time". Speaking on BBC Radio's The World This Weekend programme, he added: "Many MPs feel he has not stayed within that remit. He is not respecting the decisions that were made by the Fees Office in accordance with the rules."

Another MP, who asked not to be named, forecast that there will be "consternation" and "stupefaction" among some of the MPs who are told by Sir Thomas that they should repay money that they thought they had a right to claim.

One unnamed MP was investigated by the Commissioner of Standards, John Lyons, and cleared of wrongdoing, after a constituent had complained about newspaper reports about his expenses – and is now furious to discover that Sir Thomas has effectively overruled the Commissioner and wants him to repay some of the money. But Sir Thomas has decided that because the rules were so badly drawn up and easily bent, it is not acceptable for MPs to argue that the expenses they claimed were agreed by the Fees Office and within the rules.

MPs will have three weeks to reply to the letters they receive today from Sir Thomas. Those who are hoping to stand for re-election next year are likely to pay up immediately. But Sir Thomas's hit-list includes dozens who have already announced that they are standing down, and a small number who have already left the Commons. Others are now expected to stand down rather than weather the public storm when the full details of Sir Thomas's finding are published in December.

Disputed cases will go to the six-strong MEC, which is chaired by the Speaker, John Bercow and whose leading member is Harriet Harman, the Leader of the House. Some MPs who feel especially hard done-by may engage lawyers and try to fight Sir Thomas in the courts.

A very civil servant: The quintessential insider

Sir Thomas Legg, 74, has been a public servant for so long that when he joined the Lord Chancellor's department (now the Department for Constitutional Affairs), aged 26, the Beatles had not yet released their first single.

In 1998, he led the official investigation into allegations that British mercenaries had supplied arms for a coup in Sierra Leone, and cleared the Government of blame. This provoked Craig Murray, the former British ambassador to Uzbekistan, to describe him as "the Establishment Man's Establishment Man: as unctuous a piece of slime as ever slithered around the corridors of Whitehall".

He was embarrassed in 1993 at the Commons Public Accounts Committee after misleadingly denying judges were complaining about legal-aid cuts, when two senior judges had written to him saying just that. Since retiring from the Civil Service, his work has included stints on the House of Commons Audit Committee, and the chairmanship of the Hammersmith Hospitals NHS Trust.