The broadcaster, who hosted the programme alongside Charlie Stayt, was applauded for her interview with health secretary Thérèse Coffey.
WATCH: BBC Breakfast's Naga Munchetty applauded by fans for "brilliant" interviewing skills
The presenting duo chatted to Thérèse via video link to discuss her plans to improve patient access to GPs.
One person took to Twitter, writing: "Thérèse Coffey on BBC Breakfast, releasing a plan today to ensure patients seen within two weeks. Naga Munchetty asks where is she getting more GPs and nurse practitioners from. Mentioned nurses twice. Thank you Naga," while another added: "@TVNaga01 great questions to @theresecoffey this morning, Naga."
A third praised Naga for an "absolutely brilliant interview", while another said she did a "great job".
Naga's return comes after viewers were left questioning her absence from the morning news programme during coverage of the Queen's funeral on Monday.
Viewers praised Naga's presenting skills on Thursday's show
One person tweeted: "What have they done with Naga during all this?" while another added: "Anyone know where #Naga Munchetty was?"
While Naga doesn't usually appear on the show on Mondays, given her regular hosting slot is from Thursdays to Saturdays, the presenter took to Twitter to reveal that she was busy working on coverage of the funeral for BBC Radio 5 Live and Radio 4.
"It's been a privilege to be part of the commentary team for @bbc5live @BBCRadio4 today," she wrote. "What an honour to work with (among many other brilliant broadcasters)," she wrote on Monday, tagging her colleagues and adding the hashtag: "#queensfuneral".
Naga has been absent from the red sofa recently
It wasn't just Monday's show that Naga was absent from, however, as viewers also noticed that she was missing from the iconic red sofa last Friday.
Her absence can perhaps be explained by the fact that the funeral of former BBC Breakfast presenter Bill Turnbull was held on Friday, which she attended.
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