The presenter, 47, is usually on the morning programme with Charlie Stayt from Thursdays onwards.
While she was there as usual this Thursday (24 November), she was nowhere to be seen on Friday, with Tina Daheley filling in for her on the sofa.
Fans of the show flocked to Twitter to ask after the TV favourite, who had to leave the set early one day last week because of a problem with her voice.
"Morning isn't morning without you xx," one person posted on Twitter, adding: "Hope you're OK."
"Missed you this morning on Breakfast," said another fan of the show.
Another asked: "Where were you today?"
"Where's Naga?" said another, while somebody else wondered: "No Naga?"
One tweeted: "Is she okay?"
"Miss you," posted one fan.
Munchetty's absence comes a week after she had to leave in the middle of the show because of a "struggle with her voice".
The TV star had started the show as usual alongside co-host Stayt but some viewers noticed that she sounded as if she may have a sore throat, with one suggesting somebody could perhaps give her a Strepsil.
She then disappeared from the set and Stayt told people watching that she had "stepped away".
Sitting on the sofa alone, he said: "You may have noticed this morning that Naga has just stepped away from the sofa for a minute for a slight struggle with her voice.
"So we'll see how that works out."
Yahoo has contacted the BBC for comment.
Watch: Naga Munchetty struggles to speak on BBC Breakfast