The 45-year-old was also missing from Friday’s edition of the morning programme and was replaced by Rachel Burden.
Dan and Louise present BBC Breakfast on Monday, Tuesday and Wednesdays.
Charlie and Naga then take over until Sunday, where a host of different BBC co-presenters will step in to front the show.
The TV broadcaster has since taken to Twitter to address a viewer’s query about her absence.
Elsewhere, Naga recently took to Instagram to share a post where she revealed she felt “strong” after going for a run at the weekend.
Sharing a selfie on the picture-sharing site, the BBC Breakfast host wrote: “Cooling down with my @bbcbreakfast buddies. It’s been some time since I felt strong while running – Today was that day – Felt good.
“Maybe it was Mr Motivator inviting Charlie to workout with him in a leotard that spurred me on…? Hope you have a lovely Saturday.”
Fans flocked to comment on the post, as many people took the opportunity to compliment the presenter.