The Daily Telegraph has alleged Mr Chaytor, MP for Bury North, received nearly £13,000 for a flat in Westminster that had been paid off in 2004.
The BBC has been unable to speak to Mr Chaytor who is reportedly on a trip to the US, but the Telegraph quotes him as saying there had been an "unforgivable error in my accounting procedures for which I apologise unreservedly".
He said he would immediately arrange repayment to the fees office, according to the paper.
Former minister Elliot Morley was this week suspended from the Parliamentary Labour Party after claiming £16,000 expenses for a mortgage he had already paid off.
MPs from all parties have repaid thousands of pounds for claims made, in the week since the Daily Telegraph began publishing details of expense claims.
On Friday the Metropolitan Police Service (MPS) and Crown Prosecution Service (CPS) said the panel would hold its first meeting on potential criminal investigations next week.
The Met said it had held meetings with the CPS about expense allegations before the newspaper began its campaign, but had now decided to act.
David Cameron has made a party political broadcast about MPs' expenses
"Due to the increase in subsequent allegations received by the MPS, the Commissioner and Director of Public Prosecutions have jointly decided to convene a panel to assess allegations in order to decide whether criminal investigations should be started," a spokesman said.
Many MPs felt events were now "spiralling out of control", said BBC political correspondent Jo Coburn.
While it was known the complaints made to police could come to nothing, it came as "little comfort" to MPs returning to their constituencies on Friday, she added.
Also on Friday, Tory leader David Cameron abandoned his party political broadcast for the European Parliament Election, and instead broadcast an apology over the expenses issues, which included a pledge to "sort it out".
Liberal Democrat culture spokesman Richard Younger-Ross, Tory MP Nadine Dorries and former long-serving Labour MP Tam Dalyell are also among the latest MPs to feature in the Telegraph.
Mr Younger-Ross, who represents Teignbridge in Devon, said he had repaid more than £4,000 claimed for mirrors, a hi-fi, and a £1,475 chest of drawers for his rented London flat.
It's just like the financial crisis, there are now toxic assets in the system and the whole system is tainted by it
Mr Younger-Ross said he was given no advice on how to spend his allowances for living in London, except that it should not include luxury or antique items.
Writing in her blog, Ms Dorries rejected a string of allegations about her expenses.
The paper said she had "admitted" only spending free weekends and holidays in the property she calls her main home.
Instead, the paper said, she spent most of her time in a rented house in her constituency for which she claimed £18,000 second home expenses over two years.
She also denied allegations she had tried to claim on her second home allowance for a hotel room just before Christmas and another on New Year's Eve.
As well as Mr Morley being suspended and Mr Malik stepping down, a senior adviser to Mr Cameron, Tory MP Andrew MacKay, was forced to relinquish his post after the party said claims he had made towards his second home were "unacceptable".
Tam Dalyell told the BBC he was "entirely relaxed" about allegations in Saturday's Daily Telegraph that he attempted to claim £18,000 for bookcases, two months before he retired from Parliament in 2005.
The former father of the House said he had needed somewhere to store all the books he would be taking from his Commons office - including many years' worth of Hansard records.
Tam Dalyell said he submitted a claim for £18,000 for bookcases
He said he submitted the receipt for £18,000 to the Commons fees office and asked how much they thought it would be fair to claim - eventually, he said, they paid about £7,800 towards the bookcases.
The news that police and lawyers are to begin looking into the expenses allegations follows growing calls for a non-internal inquiry.
The Mayor of Middlesbrough and former senior police officer Ray Mallon has called for probes into potential fraud.
And the TaxPayers' Alliance has complained to police about Elliot Morley's mortgage interest claims.
The campaign group joined forces with the Daily Mail newspaper to raise funds for private criminal prosecutions of MPs, if the authorities failed to act.
'Call election' - poll
Former MP Martin Bell has said corruption is endemic in the Commons and has called for "by-elections, de-selections maybe even prosecutions" over the expenses controversy.
Interviewed for the BBC's Politics Show on Sunday, the ex-Tatton MP said Commons Speaker Michael Martin was part of the problem and "had to go".
Lord Falconer - Lord Chancellor under Tony Blair - said the situation for the whole parliamentary system was dreadful and every politician was to blame.
"We may not individually be people who have abused the expenses system, but it's just like the financial crisis, there are now toxic assets in the system and the whole system is tainted by it," he said.
Meanwhile one poll conducted for the BBC has suggested nearly two in three voters believe a general election should be called as soon as possible, following the controversy.
The ComRes survey for BBC Two's Daily Politics found 65% agreed.
A similar number - 64% - said they believed politicians "named and shamed" should be forced to quit Parliament.
On the upcoming European elections, 28% said they were less likely to vote as a result, while 25% said it had made them more eager to cast their ballot, and 47% said it would not affect their decision.
ComRes spoke to 1,011 voters between May 13 and 14.
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