The presenting duo, who have both been absent on different occasions over the past few weeks, grilled the MP following Prime Minister Rishi Sunak's announcement that the northern leg of HS2 is to be scrapped.
During one part of the interview, the presenters asked the politician about the costs involved in cancelling contracts. Watch the moment in the video below.
Taking to Twitter, now X, viewers praised Naga and Charlie's interviewing style, with one person writing: "Naga and Charlie, great interview. Holding Mark Harper accountable," while another added: "@BBCBreakfast Naga and Charlie taking no nonsense this morning #badcopbadcop love it!"
A third person tweeted: "@TVNaga01 and Charlie Stayt, credit where credits due, fantastic questioning," while another added: "@TVNaga01 Great job with Mark Harper, Charlie was as stern as I've ever seen him!"
Other viewers also commented on the fact that Naga and Charlie were reunited on the red sofa. One person tweeted: "Order is restored, Charlie and Naga are on the sofa together."
The presenters have hosted the programme together since Naga joined the line-up of main presenters in 2014. Charlie had previously presented alongside Susanna Reid before she left for ITV's Good Morning Britain.
Both Naga and Charlie have opened up about fronting the show in previous interviews, with Naga detailing her early morning routine whilst chatting to RadioTimes.com.
"My first alarm goes off at 3:45am," she said. "I have a very tight schedule, and a very organised morning, my work outfit is always laid out the night before. But I do have a system of snoozing before getting out of bed."
Charlie added: "I refuse to snooze. As soon as the alarm goes off, I am up. The other thing is, I embrace the siesta. It's become a big thing for me. I sort of sit down in the afternoon and consciously do nothing. No snooze and have a siesta, that's the formula."
Naga also revealed that she tends to receive more online abuse than her co-star. "He doesn't engage, so he doesn't see any comments," she explained. "I get more comments than Charlie but I think also that is because men just wear suits, so there isn't really too much to object to, whereas I don't wear suits and buy my own clothes. So inevitably people think they can comment on what I wear."
Naga often responds to criticism with witty remarks. In September, Naga hit back at a viewer who made a scathing remark about the black silk dress she was wearing on the show.
The comment in question read: "@BBCBreakfast What is @TVNaga01 wearing?? Looks like she's come straight to work from a night out at a sleazy single's nightclub…"
Responding with humour, Naga replied: "Sssssh... don't tell anyone. (btw - it's called a dress)."