Publicly funded promotional pictures taken by No 10 showed the Prime Minister boarding an RAF plane to West Yorkshire.
Mr Sunak spent Monday morning speaking with staff and patients at the Rutland Lodge Medical Practice in Chapel Allerton, a suburb of Leeds.
Labour accused the Prime Minister of “extravagance” in opting to fly to the city for what the party’s deputy leader Angela Rayner dubbed a “photo op”.
The transport the Prime Minister takes will vary and will always be done in the interest of what is the most effective use of his time
Prime Minister's official spokesman
It is not clear where the Prime Minister boarded the plane, but a journey from London to Leeds on the train — a distance of about 200 miles — would have taken around two-and-a-half hours.
Asked why Mr Sunak decided to fly rather than take a train, Downing Street said there was a “great deal of pressure” on his schedule.
The Prime Minister’s official spokesman said: “The transport the Prime Minister takes will vary and will always be done in the interest of what is the most effective use of his time, enabling him to get around the entirety of the UK when there is a great deal of pressure on his time.
“It will vary (depending) on what is the most appropriate use.”
The UK Government is signed up to a pledge of having a net zero carbon emissions economy by 2050.
In July 2021, ministers set out a Jet Zero strategy, containing their plans for creating a net zero aviation sector, including switching to less polluting fuels.
It did not include discouraging air travel but making travellers more aware about the emissions involved when flying instead.
Ms Rayner called on Mr Sunak to reveal how much money was “wasted” on what Labour calculated was a flight lasting just over half-an-hour.
“Families will be rightly angered by this show of extravagance by Rishi Sunak,” she said.
“Patients and staff are crying out for action from this Government in the midst of a crisis in our NHS while the Prime Minister jets from London to Leeds for a photo op.
“The Prime Minister must come clean about how much taxpayers’ money was wasted on this 36-minute plane journey for a three-hour visit at the height of a cost-of-living crisis.”
Back in London on Tuesday, Mr Sunak chaired the first Cabinet meeting of the year.
In a readout of what was said, a No 10 spokesman said Mr Sunak had touched on the five priorities he announced in his new year’s speech last week.
He told his ministers that those priorities — halving inflation, growing the economy, reducing debt, cutting NHS waiting lists and stopping small boat Channel crossings — were “not the limits of the Government’s ambition but the foundations on which we can help build a better future”.
Mr Sunak told Cabinet he wanted to “see this Government creating a more innovative economy”.
The Conservative Party leader said this included “investing in tech, seizing Brexit opportunities and backing businesses; strengthening communities, delivering world-class education; building a healthcare system focused on patients and supporting families”.
At the meeting, Chancellor Jeremy Hunt also gave an “overview of the main issues affecting the UK economy”, with the Government focused on “reducing economic inactivity”, Downing Street said.