The transport secretary Geoff Hoon claimed expenses for his constituency home while letting out his London flat and living in a Whitehall apartment.
Mr Hoon lived in a rent-free Whitehall residence while in his former post as defence secretary while the London flat registered as his "main residence" was let out to a private tenant.
This meant he was able to claim around £50,000 in allowances for his constituency home in Derby by designating it his second home.
He has defended the reports, which come just a week after home secretary Jacqui Smith was criticised after it emerged she had claimed expenses for a television package, which included two adult films watched by her husband.
'All of our customers are international and we need those transport links to be as efficient and effective as possible'
'Because key gateways have been capacity constrained, a lot of freighter services now terminate in mainland Europe'
Speaking to the Mail on Sunday newspaper, Mr Hoon said he had acted within the rules and lived in an Admiralty House apartment due to security advice.
"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 added.
He also said he did "not accept" suggestions he profited from the claims for his Derby residence.
While it is believed Conservative party leader David Cameron could announce Tory opposition to claiming second home allowances, a statement said the problems within the much-criticsed expenses system were universal.
"We are all implicated and we must all find a solution," he added.
Liberal Democrat MP Norman Baker, however, was critical of Mr Hoon's ethics in claiming allowances 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," he commented.
"Being within the rules and behaving ethically are not the same thing, unfortunately."
The Committee on Standards in Public Life has brought forward a planned report on the expenses system and will recommend changes before the end of the year.