Existing expenses rules are "threatening" MPs' family lives and their ability to do their jobs, Commons Speaker John Bercow has said.
MPs had "legitimate grievances" about how the system, in place since the general election, was working, he said.
He wants changes to rules on staff, travel and accommodation but has said the system must remain independent.
Many MPs have called for an overhaul of the rules but the expenses watchdog said it would make its own decisions.
The Independent Parliamentary Standards Authority (Ipsa), which was given responsibility for processing all claims by MPs after the 2009 expenses scandal, has said it will consider changes in some areas following widespread criticism but will "move at its own pace".
Mr Bercow's comments come in his submission to the consultation taking place on the current system.
In an eight-page letter to Ipsa, he said the previous system - under which there was widespread abuse by MPs - was "discredited" and had to be replaced.
Although the principle of independent oversight remained "sound", he said the speed at which the current system had been set up ahead of the 2010 election "had led to significant operational problems".
These were "threatening both MPs' family lives and their capacity to discharge their duties as they fully wish".
He added: "Relatively modest changes to policies on accommodation, travel, the rental of offices and the staffing of them, combined with a reasonable flexibility in the use of members' budgets, would yield real benefits to members and constituents alike.
"Similarly, a decision by Ipsa to reject extensive prescription and instead to enforce standards by audit, inspection and publication, would be a decisive step in the right direction."