MPs are due to debate the expenses review report next month
Standards watchdog Sir Christopher Kelly says he is "baffled" as to why MPs thought it appropriate to carry out a review of their expenses themselves.
The Commons Members Estimate Committee, made up of MPs, led by Speaker Michael Martin is looking into MPs' expenses.
Sir Christopher said the results of the review were unlikely to command as much public confidence as they would if there was outside involvement in it.
The MPs' report on reform of their allowance system is due in mid-June.
The review was launched after a row over Tory MP Derek Conway, who paid his son from the public purse for apparently little work. MPs will debate the report in July.
Sir Christopher, chairman of the independent Committee for Standards in Public Life, said the result may simply be "even greater distrust of the political class".
And he has pledged to launch his own inquiry if he is unhappy with the outcome of the internal audit.
"It is unfortunate that on as important an area as this, which is visible to many people and will help form people's opinions on the standards that their MPs, on as an important an issue as this, have decided to do the review by themselves without involving an independent element," he told the BBC.
He said he was sure it had contributed to trust in MPs being "diminished" - a view, he claims, a large number of MPs also share.
"The difficulty is that however well the Members Estimates Committee do their work - and I have no doubt they will do so with great integrity and objectivity - the rest of us are bound to doubt the outcome," he said.
While he had "some sympathy" with MPs who employ their spouses because of the strain the job can put on relationships, he said they needed to recognise that it was a "pretty unusual arrangement" to outsiders.
His comments follow an inquiry by parliamentary standards watchdog John Lyon into Tory chairman Caroline Spelman's employment of her former nanny and secretary.