In heated exchanges during First Minister’s Questions on Thursday, Scottish Conservative leader Douglas Ross said Mr Matheson had been “dishonest” in his claims about the data roaming charges he incurred while in Morocco over the Christmas break last year.
Mr Yousaf said he has “absolute confidence in Michael Matheson as the Cabinet Secretary for Health”.
Asked directly by journalists afterwards if Mr Matheson will still be Health Secretary at the end of the day, Mr Yousaf replied: “Yes.”
His comments came after he said Mr Matheson, who has accepted the Sim card in his device needed updating, had made an “honest mistake” and stressed the money has been paid back to the Parliament.
Mr Ross said claims it was an honest mistake were only “50% right”, as he challenged the First Minister over whether he believed the costs had resulted from parliamentary and constituency work, as Mr Matheson has said.
Data revealed by the Scottish Parliament shows in one session on January 2, Mr Matheson used 3.18GB of data, costing £7,345.689.
Mr Ross said: “It was over the Christmas break and £7,300 of that bill covered a single day, which was a public holiday.
“To put that into context, to run up those charges he would have needed to have sent 8,000 emails in that one day. That’s an email written and sent every 10 seconds continuously for 24 hours.
“All this while the Health Secretary was in Morocco on holiday.”
Mr Matheson has already said he will repay the total bill of £10,935.74, and he is also due to make a statement in the Scottish Parliament on the matter later on Thursday.
Mr Yousaf said: “There is clearly more to say on this issue. That is why Michael Matheson has agreed to make a personal statement later today.”
Mr Ross insisted the row “goes to the heart” of Mr Yousaf’s Government, as he claimed the Health Secretary has “stopped doing his job because of this”.
He accused Mr Matheson of cancelling a Government visit to a GP surgery in Glasgow because of the row, saying: “This really matters when Scotland’s NHS is in crisis and we’re approaching winter.”
He also claimed the Health Secretary had made an “attempt to dupe taxpayers out of £11,000”, saying that for “nearly a year Michael Matheson was happy for the taxpayer to pick up this bill”.
Mr Ross added: “He made no attempt to repay it until he was caught. His story is farcical beyond belief.”
He went on to attack the First Minister’s handling of the matter, saying Mr Yousaf should have immediately launched an investigation and should have “demanded that Michel Matheson hand over the device to be examined”.
The Tories have been calling for parliamentary IT staff to be allowed to examine the iPad to determine whether it was used for parliamentary work while the data charges were accrued.
Mr Ross continued: “The evidence shows that Michael Matheson claimed the £11,000 of taxpayers’ money when he knew it wasn’t for parliamentary work. It wasn’t just a mistake, it was dishonest.”
He urged Mr Yousaf to “do the right thing and sack Michael Matheson”.
But the First Minister said the charges are “a matter between Michael Matheson as an MSP and the parliamentary authorities”.
Mr Matheson has been focusing on “ensuring our NHS recovers through the course of what will be one of the most challenging winters it has faced”, the First Minister added.
Mr Yousaf told MSPs: “Honest mistakes do happen. Michael has been a member of this Parliament since its inception, all of us who have worked with him know he is a man of honesty and indeed of integrity.
“Instead of rushing to besmirch each other, perhaps our politics would be a little better if we gave each other the benefit of the doubt.”