It was the first time Ms Sturgeon had missed a Monday briefing this year, and comes just days before the First Minister is due to give evidence to a Holyrood inquiry.
The inquiry is examining the Scottish Government’s handling of complaints about Alex Salmond after he successfully challenged the government’s harassment policy and its application in the Court of Session, which ruled the investigation was procedurally unfair and “tainted by apparent bias”.
Ms Sturgeon has previously insisted there is “not a shred of evidence” there was a conspiracy against the former First Minister and has denied lying to Parliament.
She is scheduled to appear before the committee on Wednesday, and her spokesman said she “looks forward” to addressing issues Mr Salmond raised.
At Monday's briefing, Ms Freeman was asked if the reason for Ms Sturgeon’s absence was in order to prepare her evidence for the inquiry, but the Health Secretary appeared to dodge the question.
She said: “I'm sure lots of you today will have seen me doing these briefings before. I did the briefing on Friday. I have done briefings since the start of all of this, and I am doing it again today.
“The First Minister asked me to do today's briefing. I am the Health Secretary, this is a Covid briefing, it makes perfect sense."
On Friday evening, a spokesman for the First Minister said: “The people of Scotland have shown, in poll after poll and election after election, that they back the leadership of the SNP and of Nicola Sturgeon
“Today was Alex Salmond’s chance to provide proof of the conspiracy which has been alleged – and he did not do so.
“Instead, under oath, he explicitly conceded there was no such evidence against the First Minister, and also gave testimony which directly undermined some of the central planks of the conspiracy theories.“The First Minister now looks forward to addressing all of the issues Mr Salmond raised – and much more besides – when she finally gets the opportunity to address the committee next week.”