Harriet Harman has admitted that the detail of expenses claims made by cabinet ministers "looks bad".
The deputy Labour leader said that she understood that the public would be angry, after a leading broadsheet obtained receipts for ministers dating back to 2004.
The Daily Telegraph revealed that Gordon Brown paid his brother £6,577 for "cleaning services" for his private flat at Westminster, while justice secretary Jack Straw is shown to have over-claimed for both his mortgage and council tax bills.
The receipts also show that chancellor Alistair Darling changed his official second home designation four times in the four years, while business secretary Lord Mandelson claimed for thousands of pounds to improve his constituency home in Hartlepool after he had announced his resignation as an MP.
Edward Garnier, the shadow justice minister, told BBC Radio Four: "What we have learned today in the Daily Telegraph shows that we do need a more transparent system than we have now."
But Harman told the BBC that it was the House of Commons Fees Office's responsibility to decide whether MPs' expenses claims are within parliamentary rules.
"This system is that the House of Commons authorities are not to pay out on anything that is not within the rules," she argued.
"Under the system, it is up to the House of Commons Fees Office to decide whether it comes within the rules. Sometimes they will reject the claim."
She added: "We’ve agreed and we have recognised that the rules were not sufficiently clear, they were not sufficiently robust so that the public should have confidence in them, and that is why we have changed them."
The system that is being examined by the public today is not the system currently in place in Parliament, Harman said.
"We have already agreed to make many changes. What I don't want people to feel is that all MPs are corrupt and the system is rotten because I don't believe that to be the case."
She accepted that the way that the rules operated in the past has brought the system into "disrepute".
But the Commons leader continued: "In our system we do not have the level of corruption that pertains in many other countries. In our system people go into Parliament for public service.
"I know that people are angry and I know that it looks bad, but... MPs believe in the cause of public service.
"But we all realise that we have to act to win back the respect and confidence of the British people in their Parliament."
8 May 2009