But in his letter to MPs Sir Thomas said: "Some limits must be regarded as having been in place to prevent disproportionate and unnecessary expenditure from the public purse."
He has been accused of overstepping his remit - to judge claims within the old rules - but has said determining what rules were in place was "not a straightforward task".
On Thursday it emerged that Speaker John Bercow had been asked to repay £978.51 and London Mayor Boris Johnson had been asked to repay £1,266.
Prime Minister Gordon Brown, who has himself been asked to pay more than £12,000 by Sir Thomas, has urged his MPs to pay up and allow the Commons to move on from the old discredited system.
This has angered many Labour MPs who believe they have done nothing wrong and are being treated unfairly.
One Labour MP who is standing down at the next election said she did not believe Mr Brown had been "strong" enough on the issue.
"The lack of a defence, of unequivocal support, for the vast majority of people in our party has been really disappointing," Claire Curtis-Thomas told the BBC.
'Departure from justice'
She said the prime minister appeared to have been "cowed" by events, partly because he had been so personally affected by them.
Tory leader David Cameron has threatened to block any of his MPs who refuse to accept Sir Thomas's final recommendations from standing as Conservatives again.
At Business Questions in the Commons on Thursday, Conservative MP Douglas Hogg - whose expenses submissions included a receipt which listed amongst other things the cost of cleaning his moat - raised the issue.
He asked Ms Harman for a debate to restate the principle that people are "entitled to regulate their affairs according to the law, practices and rules" that exist at any particular time and that any departure from that would be a "departure from justice".
Ms Harman said Sir Thomas had been asked to look for "over-payments" - such as claims which had been paid twice, or claims towards mortgage capital payments - rather than just interest payments as allowed under the rules.
MPs would have the chance to respond to the letters over the next three weeks and could query any mistakes or "make representations" if they thought he was not judging them by the rules or standards of the time.
"Obviously we have to judge things by the rules and standards that obtained at the time, to do anything else would be arbitrary," she said.
Ms Harman did not make clear whether or not she believed that the annual limits on cleaning and gardening claims proposed by Sir Thomas were within "the rules and standards" at the time.
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