Mr Hoon was defence secretary when the claims were made
Geoff Hoon says he broke no rules in claiming second home allowances for his Derby home while living in a taxpayer-funded apartment in Whitehall.
The transport secretary lived in the flat in Admiralty House while he was defence secretary. He also rented out his own London home while there.
The revelations have led to fresh calls for MP expenses rules to be tightened.
Liberal Democrat leader Nick Clegg called it "barmy" that ministers could have two homes paid for by taxpayers.
Tory Ken Clarke said he was "shocked" by recent expenses revelations which made people think MPs were "rogues".
The shadow business secretary implied that as many as a third of MPs could have made questionable expenses claims.
He told BBC One's Andrew Marr Show that "at least two thirds of MPs I hope" were doing nothing wrong on expenses and they were suffering from "an exaggerated public view that they're all thieves, they're all rogues, they're all lining their own pockets".
Chancellor Alistair Darling told the same programme that the recent spate of revelations were "damaging".
He said: "I think we do need to get an outside examination of this and so there are recommendations coming from people who've got no axe to grind. I think that's what the public want, and they want it quickly."
Writing in the Mail on Sunday Conservative leader David Cameron said the problems in the expenses system were shared by all parties.
"We are all implicated and we must all find a solution," he said.
MPs needed expenses, but there had to be more transparency, he said. He added that if elected his party would end the policy allowing ministers with free homes to claim for a second, which he said had "no justification".
They would also ban ministers living in grace-and-favour residences from claiming second home allowances.
Kenneth Clarke on the continuing MP expenses saga
Liberal Democrat Leader Nick Clegg said it was "clearly barmy for ministers to indulge in a form of double counting that enables them to enjoy two homes at the taxpayer's expense".
"To say this is within the rules will only serve to convince the public that the rules are broken and need to be fixed as soon as possible," he added.
Prime Minister Gordon Brown has suggested scrapping the controversial second home payment for all MPs, in a shake-up of allowances.
Mr Hoon lived in an Admiralty House residence for three-and-a-half years until June 2006, while the property which had until then had been registered with Commons authorities as his main home was let to a private tenant.
He claimed allowances for the running of his constituency house in Derby by designating that as his second home.
Admiralty House, built originally as a home for the First Lord of the Admiralty, contains three apartments which are maintained by the departments whose ministers have use of them.
Mr Hoon said he went to live there on security advice.
He told the Mail on Sunday: "I was told unless I went into secure premises I would have to have round-the-clock police protection at my home in London and that that would cost the taxpayer a great deal more."
He reportedly said he did "not accept" that he was profiting from the situation.
Liberal Democrat MP Norman Baker, who once used freedom of information laws to probe parliamentary expenses, said ministers who got free properties as part of their job should not expect to get a further property from the taxpayer.
"It's quite clearly an improper use of taxpayers' money and it is not sufficient for Geoff Hoon to say he was within the rules. Being within the rules and behaving ethically are not the same thing, unfortunately."
This weekend Home Secretary Jacqui Smith has said her marriage is "strong" despite revelations she claimed expenses for adult films watched by her husband.
Ms Smith is also being investigated by the parliamentary commissioner for standards over her decision to claim at least £116,000 in second-home allowances for her family home.
Meanwhile she stated her main residence - the one at which she spends most time - as her sister's home in London, which she shares during the week.
Employment Minister Tony McNulty is also being investigated after it recently transpired that, until January, the MP had claimed up to £14,000 a year since 2001/2, for a home in his Harrow East constituency where his parents live.
The Committee on Standards in Public Life has said it will bring forward a wider inquiry into MPs' expenses, with a report due towards the end of the year.
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