The expenses claims which MPs make must be based on the "spirit of what is right", Michael Martin has said.
Making a statement in the Commons, the Speaker called for "serious change" to the system of MPs' allowances.
Amid continuing disclosures of claims made by MPs, the members estimate committee, which oversees the system, is backing an emergency overhaul.
An "operational assurance unit" will ensure there is independent oversight of claims, Martin said.
"But working to the rules and the rules alone isn't what is expected of any honourable member," he added.
"It is important that the spirit of what is right must be brought in now."
There had been reports that privatising the Fees Office could lead to expenses claims being exempt from freedom of information legislation.
But that option was rejected both by Number 10 and by senior MPs.
The Speaker also said that the leak of confidential data on MPs' expenses may have involved a criminal offence.
Martin said there is a basis for considering that a criminal offence may have been committed when personal data was passed to the Daily Telegraph.
He confirmed that the Clerk of the House had been advised that there was no basis for a court injunction to stop revelations about MPs' expenses.
But the Speaker confirmed that the Clerk had asked the Metropolitan Police to look into how the details of the expenses had been published before the scheduled announcement in July.
Martin also said there were security implications, including the potential for MPs' bank account details to be disclosed.
He said that he would be writing a letter to the newspaper's publisher raising these issues. "The letter will be copied to all national newspapers," Martin told MPs.
Martin continued: "I can understand members' concerns about the revealing of details of bank accounts, style of signature, verbal passwords and that an individual who may have sold the data is also capable of selling this information further. This is why the police have been informed.
"I am also writing to the publisher of the newspaper drawing this fact to their attention and reminding them of the serious security implications if personal data, which might expose members and others to risk to their safety, were to be published."
In sometimes heated exchanges following the statement, Martin admitted to the House that he "might be in a bad mood today".
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