John Swinney has "staked his reputation" on defending Michael Matheson, according to the Scottish Tory leader Douglas Ross.
Speaking at the Kelpies in Mr Matheson's constituency, Mr Ross said the former healh secretary - who quit earlier this year amid an investigation into his £11,000 iPad expenses - should stand down and accused the SNP of "rallying around defending him".
"The Scottish Conservatives are bringing forward a vote this week urging Michael Matheson to resign so we can have a by-election here in Falkirk West on the same day as the General Election," he said.
"I think every MSP should consider their vote on Wednesday," Mr Ross added. "This is something that John Swinney has staked his reputation on. He would rather support his good friend than defend the integrity of parliament.
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"Michael Matheson lied to Parliament, he lied to the Presiding Officer and, most importantly, he lied to the public."
The First Minister, he added, has "made Michael Matheson out to be the victim here".
But Mr Swinney said as First Minister he must ensure "everyone is treated fairly whoever they are".
He reiterated his belief that the Holyrood committee which has recommended a 27-day Holyrood suspension for the former health secretary, as well as a 54-day loss of wages, did so after a process which was "prejudiced" by comments made by Tory MSP and committee member Annie Wells.
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That was the recommendation made by MSPs on the Scottish Parliament's Standards Committee, who conducted a probe after Mr Matheson racked up data roaming charges of almost £11,000 on his parliamentary iPad.
He initially claimed he had done this while using the device for work purposes on a family holiday to Morocco - but later confessed his teenage sons had used the device as a hotspot so they could watch football during the trip.
While Holyrood still has to vote on the sanctions to be imposed on Mr Matheson, the Tories are also set to force a vote in Holyrood, calling on him to resign as the MSP for Falkirk West.
They are pushing for a by-election in the constituency to be held on July 4 - the same day as the General Election.
The vote is unlikely to pass due to a lack of support from the Scottish Greens, with party MSP Ross Greer calling it "cynical".
Ms Wells said in November Mr Matheson's explanation was "riddled with lies", but the Tory leader rejected the claims her comments prejudiced the inquiry.
It was the Scottish Parliamentary Corporate Body (SPCB) - a cross-party group of MSPs tasked with the running of the Parliament - who found Mr Matheson to have breached the MSP code of conduct, Mr Ross said, claiming Ms Wells did not know the matter would appear before her committee when she made the comments.
Mr Swinney said Ms Wells having spoke out against Mr Matheson before the committee reached its conclusion gave him "deep concerns" about the process that he could not ignore.
Speaking to journalists as he campaigned in Dumfries, the First Minister said: "I just feel I have got to point out something I think is wrong with the Parliamentary process.
"I don't think it would say very much about me if I just turned a blind eye to something that in any other walk of life people would be raising deep concerns about.
"In any other field if somebody prejudiced a process there would be enormous concern being raised and I don't think it would say very much about me if I ignored that."
Mr Swinney continued: "I think a First Minister's job is to make sure there is fairness for everybody in Scotland, that is everyone is treated fairly whoever they are.
"When I said I would be the First Minister for everybody in Scotland, that is what I meant.
"So, what sort of First Minister would I be if I just ignored the fact that there is a prejudicial process that is going to be put to Parliament?"
He insisted the "process that has been undertaken has been prejudiced" because Ms Wells made comments on the case, but then remained on the committee as it ruled on the matter.
The SNP leader pointed out: "Another Conservative MSP, Stephen Kerr, made comments and recused himself. So, the precedent has been set that you shouldn't make comments about a case and then participate in its deliberations.
"That is the issue I have raised, which is why I cannot support the sanction that has come out of that process, because I think the process is prejudiced."
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