MSPs have awarded themselves a £1m increase in allowances for employing staff and running their offices.
It will be shared out between members - despite a recommendation constituency MSPs should be better funded than those elected from the regional lists.
The call caused long-standing differences between the two types to bubble to the surface - with claims of an "offensive" two-tier system.
It came as MSPs voted to overhaul the allowances system.
An independent probe on the subject by Dundee University principal Sir Alan Langlands proposed the two-tier system - a distinction which he said reflected bigger workloads.
Labour supported the recommendation - but the SNP argued in favour of splitting the difference to give both types of MSP an annual limit of £54,562 for staff salary costs, which won support from the Conservatives and Greens.
"I find this offensive and contrary to the principles that all members are equal"
But Michael McMahon, Labour MSP for Hamilton North and Bellshill, told an earlier parliamentary debate: "A very worrying precedent will be set if this crafty coalition get their way - rip up an independent, evidence-based report and pick-pocket from hard-working staff of constituency members."
Sir Alan recommended a maximum of £62,000 for staff salaries for constituency MSPs, which adjusted upwards for inflation would now be £64,300.
And he said staff salaries for regional list MSPs should be limited to £45,000, now increased to £46,700 - a distinction which he said reflected bigger workloads.
But Liberal Democrat West of Scotland MSP, Ross Finnie, said he would not support a move to make him a "second-class citizen".
'Founding principles'
The former environment minister said: "I find this offensive and contrary to the principles that all members are equal, unless someone can produce some substantial evidence to demonstrate the contrary - that is not present in the recommendations of this report."
The SNP's Trish Marwick, who holds the seat of Central Fife, said all MSPs should be equal, regardless of how they were elected.
She told the Holyrood chamber: "There should not be any disparity in the status of constituency and regional members. It is one of the founding principles of this parliament."
Parliament also agreed to abolish mortgage-interest payments for MSPs from outlying areas who buy a home in Edinburgh and to establish a register of family members employed by MSPs.
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