Five MSPs each ran up £80,000 in expenses last year, according to the latest statistics.
The cost of running the parliament was amost £48m
The salaries of 129 MSPs totalled £9m, the annual report by the parliament's Corporate Body has revealed.
The statistics show that MSPs claimed £7.5m in expenses in 2002 - £300,000 more than the previous year.
Tories Alex Fergusson and David Mundell, Liberal Democrats Jamie Stone and George Lyon and Labour's Alasdair Morrison were the highest earners.
Mr Fergusson, now MSP for Galloway and Upper Nithsdale, claimed £81,549
This included £42,241 to cover office costs, £9,523 for accommodation in Edinburgh, £11,050 in travel expenses and £11,205 for stationery.
Mr Mundell, a list MSP for the South of Scotland, claimed £80,327, including £10,498 in travel costs and £14,403 for office supplies.
The travelling expenses for Mr Stone, Mr Lyon and Mr Morrison were higher because they represent large, remote constituencies
Sir David Steel claimed £34,925 and Tory MSP Bill Aitken £35,037.
Shetland MSP Tavish Scott claimed the most in travel expenses at £23,230.
Scottish Socialist Party leader Tommy Sheridan and his Green counterpart Robin Harper were the only MSPs who claimed the full £50,700 support allowance.
Parliament spent £47.9m on running costs in 2002/2003, which included £9.1m in MSPs' salaries.
Twenty six MSPs who either lost their seats or quit parliament at the last election received a total of £626,964 in "resettlement
In the report, Presiding Officer George Reid acknowledged the "frustrations" associated with the continuing delays and rising costs of the Holyrood building project.
But he said interest in the on-site visitors centre has been "extremely positive and encouraging".