Gordon Brown warned that politics must be "cleaned up" as scores of MPs - including himself - were expected to be sent letters by auditors asking them to repay money from the past five years.
The Prime Minister said Sir Thomas Legg, the former civil servant charged with a review into MPs' expenses, had probably introduced new rules retrospectively so that MPs who had filled in their forms correctly may have to pay back money.
"We have got to clean up politics, we have got to consign the old discredited system to the dustbin of history, so this is part of the process of doing so," he told GMTV.
"Sir Thomas Legg will make recommendations, people have a chance to look at what he says, then my advice to people is, if after the process has gone through in the next few weeks, he says you have got to repay, let's get it done, let's get it sorted out and let's get it back to a system that people can make sure they have confidence in."
The Prime Minister's remarks come as the Daily Telegraph reported that he could be asked to repay more than £5,000 in expenses, including claims for cleaning his London flat and constituency home. There are signs that many could choose to fight the findings of the review, with a senior MP, Sir Stuart Bell, warning that his colleagues would not tolerate being treated "unfairly".
Speaking on GMTV, Mr Brown said: "He (Sir Thomas) is an auditor, looking at the expenses. I think he has probably created new rules going backwards, in other words retrospectively introduced new rules, so people who were doing everything right may have to pay back even although they have filled in their forms correctly.
"So that is what he is going to do, but if he does it, and people can question it and go through the process, once it is finished, let us get it over with, let us get people repaying money that he says is due and let's make sure that people are satisfied that the system is now the right one."
Mr Brown added that it was "pretty different" from previously to change the rules retrospectively and people would have "some questions about that". But he said he believed the system needed to be "sorted out" so that the public had confidence in it.
Asked if he had received his letter yet from Sir Thomas, Mr Brown said: "I expect I will get one, most MPs are getting one, and I will do whatever is necessary, we have got to get the system sorted out."
Responding to a question as to whether he would pay back money, should he be asked, Mr Brown said: "If he asks me to do so and if we have answered all the questions, yes, of course and that is the right thing to do."