But the Tory leader publicly slapped down the multi-millionaire MP and said Mr Duncan had made a 'bad mistake' in moaning about how MPs have been treated following the expenses scandal.
Mr Cameron told reporters in his Oxfordshire constituency: 'I spoke to Alan Duncan yesterday and made it clear in no uncertain terms that when it comes to the mess of expenses, the words we use, just as the actions we take, have got to demonstrate completely that we share the public's real fury at what went on in parliament.
'Alan made a bad mistake and he has acknowledged that, he has apologised and withdrawn the remarks.'
Mr Cameron went on: 'He's withdrawn those remarks he shouldn't have made, and I think we should leave it at that.'
Mr Duncan, who is thought to be worth £2.1million, had been secretly filmed claiming no 'capable' person would want to enter Parliament when MPs are treated 'like s***'.
Mr Duncan is the face of the Tory Party on issues of MPs' expenses, making his outburst all the more embarrassing for David Cameron.
Mr Cameron arrived back in his Oxfordshire constituency today after a ‑10-day break in
His holiday was disrupted yesterday when he authorised a damage-limitation exercise by aides over the affair.
Although Mr Duncan initially claimed his remarks were a joke, Mr Cameron treats the subject of MPs expenses 'very seriously', one ally said, and took a 'dim view' of the shadow minister’s secretly-filmed comments.
Mr Duncan is one of only two Conservatives on the House of Commons Commission, the body which oversees the expenses regime - and has the task of cleaning up the failed system.
But there are suspicions Mr Duncan's comments simply reflect the attitudes held privately by many MPs.
While they have appeared apologetic on the surface, it is feared many feel aggrieved by the public backlash against what they believe were reasonable expenses claims.
As Alan Duncan’s future hangs in the balance, another Tory MP, backbencher Anne Main, was preparing for a deselection vote by her constituency party tonight.
Ms Main, the MP for
her grown-up daughter to live rent-free at her taxpayer-funded second home.
Her case is being investigated by the Parliamentary Commissioner for Standards but some local Tories believe her 1,361 majority could be wiped out by the allegations.
A meeting of St Albans Conservative Association’s ‑‑ members has been called to decide whether Ms Main should be able to stand as their MP at the forthcoming general election.
It is understood that the 52-year-old MP, who won the seat from Labour in 2005, will address the meeting before an association spokesman does likewise.
Members will then be asked to vote on whether to deselect her.
A Conservative Party spokesman said that the issue was a 'matter for the local association'.
Mr Duncan's remarks were recorded by Heydon Prowse, an activist who dug a pound sign in Mr Duncan's lawn earlier this year in protest at his £4,000 expense claims for gardening - which he was forced to repay.
Mr Duncan invited Mr Prowse to Parliament in July as a goodwill gesture but did not know he was being filmed.
Mr Duncan said: 'No one who has done anything in the outside world, or is capable of doing such a thing, will ever come into this place ever again, the way we are going. Basically, it's being nationalised, you have to live on rations and are treated like ****.'
The comments threaten to undermine the hardline stance taken by Mr Cameron, who has ordered his MPs to pay back thousands of pounds in expenses and barred some from standing again as Tory candidates.
One senior insider said: 'Nobody knows what the future holds. But David is taking a very dim view of this.'
Labour MP Sir Stuart Bell, who sits on the ruling Commons Members Estimate Committee with Mr Duncan, later lambasted him as 'arrogant and out of touch'.
'Not only has Alan Duncan been a roadblock to reform, he has now shown how arrogant and out of touch he is,' he said.
'How can David Cameron keep him in a job so closely involved with MPs' pay and allowances?
'Cameron talks a tough game on expenses but it is clear there's one rule for the Tory backwoodsmen and another for his friends in the Shadow Cabinet.
'I will be writing to the Speaker of the House pointing out the difficulty of Alan Duncan remaining in his position as chair of the Audit Committee when his personal views are contrary to those of the majority of MPs who want to see the system cleaned up.'
Mr Duncan - who is on holiday - yesterday issued a swift apology. In a statement, he said: 'The last thing people want to hear is an MP whingeing about his pay and conditions.
'It is a huge honour to be an MP and my remarks, although meant in jest, were completely uncalled for. I apologise for them unreservedly.'
But it was not the first time he has been forced to grovel over the expenses scandal - leaving him open to charges of hypocrisy.
The MP for
He was also ordered by Mr Cameron to pay back more than £4,000 in gardening expenses after it emerged that he tried to claim for expenses such as repairs to his ride-on lawnmower.
But Mr Duncan also appeared unrepentant about those claims during the short video published yesterday on the website of Mr Prowse's magazine, Don't Panic.
He said: 'I spend my money on my garden and claim a tiny fraction based on what is proper. And I could claim the whole bloody lot, but I don't.'
Asked how much he spent on the garden, Mr Duncan replied: 'About £2,000 a year and this was £1,000 a year on expenses, you know. It's just, I'm afraid the world has gone mad.'
Fellow Conservative MP Nigel Evans was also caught joking that he couldn't survive on the MPs annual salary of £64,000.
Commenting on sandwiches which he was eating, Mr Evans said: 'I made these myself. It's my second job! Got to have a second income mate, couldn't survive on 64.'
Mr Duncan, who is in a civil partnership with his partner James Dunseath, is fast turning into a political liability for the Conservative Party.
Earlier this year, he caused uproar after he joked that he would like to murder Miss
Business Secretary Lord Mandelson last night seized on the comments as proof that the Tories were privately opposed to reforms of the expenses system.
He said: 'I don't know what sort of joke he is trying to make in private.
'I think, rather more seriously, he, as the Shadow Leader of the House, has not exactly been helpful - and I say this frankly about him - in bringing about the reforms that the Government has tried to introduce.
'I must say, Alan Duncan is very fond of speaking a good game publicly, but in private talking and acting quite differently. So I'm not surprised he has been found out.'
Mr Prowse, 28, filmed Mr Duncan on a secret buttonhole camera which he had activated in the House of Commons' toilets.
He said: 'What we captured was the general prevailing attitude in the Commons that he didn't take the whole expenses scandal particularly seriously. For a man who is leading the Tory charge on expenses, he didn't seem bothered about the whole thing.
'He seemed to think that MPs have been persecuted and have done nothing wrong.'
Liberal Democrat MP Norman Baker said that Mr Duncan's comments had exposed the 'hypocrisy' of the Tories over the expenses scandal.
'While they claim in public that they want to clean up politics, they let their true feelings show as soon as they - mistakenly - believe the cameras have been switched off,' he said.
