Sir Thomas Legg has ordered 390 MPs to repay over £1million.
His final report into expenses means more than half of Parliament will pay back taxpayers cash.
Legg has pointed out that a "lack of evidence" especially on mortgage interest payments meant claims could not be scrutinised, there was a "lack of transparency" in the system and a "culture of deference".
In a damming indictment of the 'old boys' network he said the Fees Office was "influenced" by MPs from the Speaker down.
He wrote in his executive summary that MPs thought their claims were "self certified".
In all 52% of MPs will be asked to repay money, three repayments total over £40,000 and there have been 44 successful or partially successful appeals, 56 MPs were recommended to repay between £40,000 and £5,000.
The £1.3m after auditing claims dating back to 2004 - the investigation cost £1.6million.
"Payments by the Fees Office which contravened these requirements breached the published rules and standards in force at the time. To hold such payments invalid is not to impose new rules retrospectively, but to apply now the rules that were properly in force then, but were overlooked or misunderstood at the time.
"For this reason, the fact that in some cases the Fees Office and MPs acted in apparent ignorance of the rules and standards then in force cannot cure the invalidity of the payments.
"Suggestions that MPs necessarily acted 'in accordance with the rules' simply because the Fees Office made payments to them, and even encouraged and endorsed their claims, are therefore misconceived."
Some MPs say the way Sir Thomas carried out the audit was "sloppy" and £180,000 was cut off the total after appeals.
Sir Thomas also said £800,000 has been repaid already - some voluntarily - in the months since the scandal broke.
He has called the expenses system "deeply flawed" .
Londoners were outraged that MPs living in outer London claimed for a second home allowance, a practice now outlawed.
Legg indicated it could:
"...only be used as reimbursement for specific and proportionate expenditure on accommodation needed for the performance of Parliamentary duties".