Four top officials are leaving the MPs' expenses watchdog after a spat with Commons Speaker John Bercow.
All but one of the five members of the Independent Parliamentary Standards Authority (Ipsa) board will quit in January.
They refused to reapply for their posts after Mr Bercow declared they could not have their terms automatically renewed, as had been expected.
The four will now be replaced with people chosen under the Speaker's own system, sparking questions about Ipsa's independence.
Ipsa chairman Sir Ian Kennedy warned the new members would be seen as "placemen" and of the risk of exposing the watchdog to "political influence".
The row erupted after Mr Bercow wrote to Sir Ian in April, noting that the Parliamentary Standards Act 2009 required a "fair and open competition" for each board position at the end of a fixed term.
But the Ipsa chief replied, dismissing the idea that the Speaker needed to hold a full selection process - which is estimated to cost £100,000.
He also raised concerns about the "perception" that Mr Bercow was seeking to neuter Ipsa by turfing out Sir Scott Baker, Jackie Ballard, Ken Olisa and Isobel Sharp "wholesale" in January.
Sir Ian said: "It is in nobody's interest for expenses once again to become a live issue in the shape of a debate about the future composition of the Board and what this might say about Ipsa's role as an independent regulator.
"I make no apologies for pointing out the fact that there is much at stake here, not least the reputation and future standing of Ipsa and indeed the reputation of parliament itself."
Sir Ian argued that the need for a full selection process only applied to initial appointments and were otherwise only usually held if a member had been considered "unsatisfactory".
He insisted there was "no good reason" for shaking up the appointments process and warned new board members would be seen as "placemen/women of Parliament".
"This would be wholly undesirable given the need for Ipsa to be and be seen to be independent of political influence," he wrote.
Despite his warnings, a new appointments process was launched in August and the successful candidates are due to be announced soon.
It is understood that although Sir Ian did not agree with the decision to stage it, he believes it has been conducted fairly.
Ipsa confirmed the independent board members had not reapplied for their posts and that the changes had played a part.
"These are individual choices but one contributing factor was their concern about the process used to appoint and reappoint members to the Board," a spokesman said.
The Speaker's Office played down the row, insisting it was only a disagreement over the legal interpretation of the Parliamentary Standards Act.
But a spokesman confirmed it had declined a request from Sir Ian to seek legal advice on the meaning of the legislation.
Ipsa took charge of MPs' expenses in 2010 but tough new rules sparked fury among many politicians. Although parts of the new system have now been eased, there are still tensions.
The regulator is currently carrying out a review of MPs' pay, amid calls for salaries to be raised, and has already signalled that gold-plated pensions will be slashed.