Some MPs accused the Fees Office of encouraging big expense claims
The man who oversaw the discredited MPs' expenses system got an 8% pay rise last year, Commons accounts show.
Director of Resources Andrew Walker's salary rose from a band of £115,000 - £120,000 to £125,000 - £130,000.
An 11% rise for the most senior Commons official, Malcolm Jack, means he now earns more than Gordon Brown.
His pay rose from a £170,000-£175,000 band to £190,000-£195,000. He also got an increase in benefits in kind from £20,000 to £25,000.
The increases were reportedly approved by a senior pay panel, but they come at a time when others in the public sector are seeing their annual salary rises restricted to about 2%.
BBC political correspondent Carole Walker said it was unclear whether the rises were agreed under the previous Commons speaker Michael Martin, who stepped down following the expenses row, or had been voted upon more recently, since officials vowed to clean up the system.
Mr Walker was the official who defended the Commons' position at an information tribunal last year, when it was resisting publishing full details of MPs' expenses claims.
When details were eventually published, after being leaked to the Daily Telegraph, many MPs justified their claims by saying they had been within the rules and agreed by the Commons Fees Office.
But amid public furore over some of the claims made under MPs' second homes allowances, new interim rules were brought in to limit their use and an independent inquiry is currently considering what changes need to be made.
Mr Jack, the Clerk of the House, is responsible for ensuring pay levels are broadly in line with the civil service.
The biggest rise went to Joan Miller, who runs Parliament's IT systems. Her pay rose from between £90,000 and £95,000 to a pay band of between £105,000 and £110,000.