The proposal was made at Holyrood by cross-party members looking at wider sanctions available if politicians are sent to prison.
Walker, 71, of Alloa in Clackmannanshire, is due to be sentenced later this month for 24 offences spanning almost three decades, following a trial at Edinburgh Sheriff Court.
The Dunfermline MSP carried out the attacks against his three ex-wives and a stepdaughter between 1967 and 1995.
His refusal to step down has sparked anger among the public and politicians.
Presiding Officer Tricia Marwick alerted MSPs to the proposal by the Scottish Parliament's corporate body (SPCB).
"We recommend that 90% of salary should be withheld for the duration of imprisonment," she wrote in a letter to MSPs.
"I shall therefore be seeking the parliamentary bureau's agreement to bring forward a resolution before parliament next week to amend the salary scheme.
"In recommending this course of action to parliament, it should be made clear we do not seek to encroach upon the role of the courts. Our approach should in no way be interpreted as a punishment - that is for the courts."
The change can be made by resolution of the parliament under section 81(1) as read with section 83(5) of the Scotland Act 1998, she said.
The former SNP MSP, who was ejected from the party when the allegations surfaced, denied the charges.
The law states that any elected member jailed for more than one year will be disqualified. In summary cases heard in sheriff courts in Scotland, the maximum sentence that can be handed down is one year, allowing Walker to remain as an MSP even if he is jailed.
The Scotland Act gives the Scottish Parliament the power to set pay provision, meaning changes could be made by MSPs without referring to Westminster.
Disqualification of a member is a matter for the UK Parliament.