MPs will be forced to repay all expenses claims identified as excessive in a controversial audit, it has emerged.

Their allowances will be docked if the fail to accept the findings of an inquiry by Sir Thomas Legg, who has ordered hundreds of MPs to repay expenses claims.

Sir Thomas’ investigation was supposed to draw a line under the expenses scandal by exposing excessive claims made by some MPs - and allowing others to say they had been given the all clear.

But there was fury at Westminster when he wrote to every MP revealing his findings.

Some were told they had spent too much because Sir Thomas imposed an annual limit of £2,000 for cleaning bills, although the limit did not exist when the bills were paid.

Others insisted his conclusions were simply wrong, or unreasonable.

Conservative Shadow Minister Caroline Spelman (Con Meriden) was told to repay £1,600 because she claimed for his mobile phone bill using the wrong form. There was no suggestion the claim itself was improper,

Cabinet Minister Liam Byrne (Lab Hodge Hill) was told to repay a £1,869.54 mobile phone claim for the same reason.

Lynne Jones (Lab Selly Oak) was asked to repay £800 after wrongly claiming twice for a new radiator in August 2005 - but she had already repaid the money before Sir Thomas’ inquiry began.

Every MP was offered a chance to respond and contest the findings.

But if Sir Thomas rules that they must pay the money back, they will be forced to do so whether they agree with his conclusions or not, after the Commons Members’ Estimate Committee, chaired by Speaker John Bercow, ruled that they should have it docked from future allowances.

The MEC will also be setting up an independent appeals process for MPs who believe there are “special reasons” why they should not pay.

But, in a statement, the MEC said: “It is intended to be an appeal process in respect of individual cases and not to reopen Sir Thomas’s review as a whole.”

Notice of an appeal must be submitted by December 14 and the substance of the appeal a week later.

Appeals will be considered by Sir Paul Kennedy, who is a barrister and the Interception of Communications Commissioner. The procedure is meant to be brisk and completed by early 2010.

The publication of Sir Thomas’s report on the findings of his audit this summer will not now be published until after any appeals have been dealt with.