William and Kate, joined by Prince George, Princess Charlotte, Prince Louis and their nanny Maria Teresa Turrion Borrallo, travelled on a £73 FlyBe flight from Norwich to Aberdeen this morning, it was reported.
They were heading to Balmoral for their annual break at the Queen's retreat in the Scottish Highlands.
Kensington Palace declined to comment.
Harry and Meghan have faced criticism for taking four private jet journeys in 11 days, despite their environmental campaigning.
On Thursday, the SussexRoyal Instagram account shared an image of cupcakes bearing the mantras "stay strong", "you are enough", "you are worthy" and "you are so loved", among others.
It was part of a post highlighting Luminary Bakery, a social enterprise in Stoke Newington, north London, which helps women from disadvantaged backgrounds who have faced traumatic experiences get their lives back on track.
Meghan, in a quote posted alongside the image, described it as a "space for baking, healing and rebuilding" and revealed she had secretly visited the bakery.
She added: "When I visited the women earlier this year, I was struck by how the baking, itself, is a means of therapy for these women - which in many ways makes complete sense - feeling they had no control over their lives based on their previous (and often harrowing) circumstances, they found comfort in the measured nature of baking."
The post, taken as a sign the duchess is focusing on her charity work rather than the jet row, followed a behind-the-scenes video that Meghan released on Wednesday of a photo shoot for a capsule clothing collection for the charity Smart Works.
Celebrities including singer Sir Elton John, pop star Pink and chat show host Ellen DeGeneres have all publicly defended the duke and the former Suits actress.
Sir Elton revealed he provided Harry and Meghan and their baby son Archie with a private flight to Nice to "maintain a high level of much-needed protection".
The star condemned the "relentless and untrue assassinations on their character" and wrote on social media that he had made sure the flight was carbon-neutral by making the "appropriate contribution" to a carbon footprint fund.
Actress Jameela Jamil claimed, as she also backed Harry and Meghan, that it was not safe for the public to fly on planes with the royals, tweeting: "It's not safe for us to be on the same planes as royals or presidents you absolute muppets.
"They are prime targets for kidnap and sometimes assassination.
"It's in the interest of us civilians to not be endangered by proximity to people in such powerful positions."
The Sussexes' trip to Nice followed a reported holiday to Ibiza to mark the duchess's 38th birthday earlier this month.
Pink said Meghan has been subjected to "the most public form of bullying I have seen in a while" and called on people to show "it's cool to be kind", while DeGeneres said the royals are "the most down-to-earth, compassionate people".