Gordon Brown declared that Speaker Michael Martin's fate was in the hands of MPs, as they waited for him to put his case in the Commons.
The Prime Minister called for "root and branch reform" of the expenses system, but when invited to back Mr Martin said simply: "The decision on who is Speaker is a matter for the House of Commons."
Mr Brown has previously praised Mr Martin as doing a good job, but that formula has now been dropped both by the premier and his spokesman.
Mr Martin also faced the prospect of a motion of no confidence in him being tabled at Westminster and Mr Brown's spokesman said: "The Prime Minister and the Government will support the will of the House."
Speaking at an event in north London to mark the launch of the Government's car scrappage scheme, Mr Brown said: "The decision about who is Speaker is a matter for the House of Commons. It could never be a matter for the Government."
He added: "What we have seen in expenses and in the revelations has angered and appalled me. It has angered me because people expect politicians to be serving the public and not serving themselves. It has appalled me because I was brought up to believe that we must have the best standards in public life.
"So there has got to be fundamental change. We are no longer talking about papering over the cracks. We are no longer talking about a minor change here or there.
"There has got to be root-and-branch reform and I am hopeful that we can get a consensus in this country about what is needed to be done to have a complete clean-up of the political system and to make sure that people can have trust in what their politicians do.
"Some MPs are doing a very, very good job - indeed most of them are. But where there are faults, and where there are failings and where people are responsible, they have to accept that there will be disciplinary action. We will cut the expenditure on these items and at the same time we will have a wholesale root-and-branch reform of the system."
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The motion of no confidence in Mr Martin was tabled by Conservative MP Douglas Carswell, and signed by 15 MPs from the three major parties. The Harwich and Clacton MP said he had been told by the Commons authorities that it was for the Speaker himself to decide whether to call it for debate in the chamber.
