Uddingston and Bellshill MSP Michael McMahon, who has been suspended for a day, shouted the comment at Tricia Marwick.
It came after it emerged the Parliament's official report had to be corrected because First Minister Alex Salmond told MSPs there were about 18,000 people employed in renewable energy across Scotland, when the total is closer to 11,000.
The Tories raised that issue in Holyrood yesterday afternoon, shortly before the close of business. But there were protests from some MSPs when the Presiding Officer tried to move to the next item on the agenda.
After Ms Marwick called for order, it is understood Mr McMahon said "You're out of order" to the Presiding Officer.
She demanded Mr McMahon withdraw the remark and he apologised immediately to her.
Ms Marwick then asked him to come to her office after the close of business at Holyrood yesterday and suspended him.