Many backbenchers are livid, saying they are now being told by Sir Thomas to repay claims that were allowed at the time by Commons officials.
But Sir Thomas's letter said that there appeared to have been no limits for services like gardening and cleaning and "some limits must be regarded as having been in place, to prevent disproportionate and unnecessary expenditure from the public purse".
Labour MP Bill Etherington, 68, who is standing down at the next election told his local paper the Sunderland Echo :"If he has decided I shouldn't have claimed something which I feel was justifiable under the rules at the time, then I won't pay it.
"If I don't think it's correct they can take the matter to court."
Sir Thomas cannot force MPs to repay any money and his recommendations will be put to the Commons' Members Estimate Committee, which will decide what to do next.
Deputy Labour leader Harriet Harman told a meeting of about 40 Labour MPs on Tuesday morning public confidence must be restored in the expenses system.
But she said the letters were just the first stage of the process and said there was "no conclusive determination" in them and MPs had been invited to respond.
EXPENSES: THE STORY SO FAR
MPs are allowed to claim expenses for running a second home but there was much uproar in May when receipts and details of what they had been claiming for were leaked to a newspaper.
Among them were claims for expensive TVs and furniture, MPs who claimed for more than one property by "flipping" the designated second home and others who over-claimed for mortgages or services.
Many MPs have announced they will be standing down, some have already repaid claims in response to constituents' anger.
Party leaders pledged to change the system and an independent review is due to make its recommendations this month.
The PM also asked an independent auditor, Sir Thomas Legg, to go over past claims again, to ensure money had been paid out properly. MPs have been getting his letters saying how much they should pay back...
The BBC's deputy political editor James Landale said some Labour MPs were planning to challenge any requests for money while others were angry at the Parliamentary Fees Office which they say has lost some of the receipts.
One former minister said he had yet to receive his letter and the way they had been sent out was a "complete shambles". Another Labour MP said it appeared Sir Thomas was "impugning all our integrity and that matters".
The Financial Times reports that angry backbench Labour and Conservative MPs were planning to meet to discuss what to do about the review.
David Cameron has been asked to provide more information about mortgage payments, Lib Dem leader Nick Clegg is to repay £910 relating to gardening claims and the SNP's Alex Salmond is repaying £710 for removal costs.
Business Secretary Lord Mandelson is repaying £800 claimed for the cost of tree surgery work in his Hartlepool home in 2004.
Veteran Tory MP Ann Widdecombe, who is stepping down at the general election and had one of the lowest claims under the second homes allowance last year, said there was a "pretty big question mark over the legality of this".
"If any other employer said to his employees: 'These were the rules. You stuck fastidiously by them ... but we have now changed the rules so here's a bill', that employer would be up before a tribunal," she said.
Labour's Sir Stuart Bell, a member of the Members' Estimate Committee, said talk of MPs preparing legal action to fight repayments was "balderdash".
Gordon Brown: "People must abide by the decisions that are made"
But he said applying caps retrospectively was against the "rules of natural justice".
Lib Dem MP Norman Baker, a long time campaigner for more expenses transparency, told the BBC MPs had to "take the rough with the smooth" but said he was concerned that mistakes had been made in the rush to act, as he had been asked for more information to justify his mortgage interest payments.
He told the BBC: "I've never claimed for a mortgage ... I've deliberately not done that as a matter of principle, so it seems to me some of the information he's basing his statements on is completely inaccurate."
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