Downing Street said Rishi Sunak flew to Leeds from London on an RAF jet because it was the "most effective use of his time".
The prime minister has been criticised for making a 36-minute trip from RAF Northolt in west London to Leeds Bradford Airport on the small plane on Monday morning to visit a West Yorkshire healthcare centre.
Downing Street posted a photo of Mr Sunak boarding the plane as the sun rose before it set off at 7.47am, according to flight tracker data.
He then landed in Leeds at 8.23am before the plane returned three and a half hours later, landing at Northolt at 12.25pm.
Its tail is emblazoned with the union flag and has King Charles' Royal Seal on the fuselage as well as the RAF logo.
Mr Sunak's spokesman said the PM had flown instead of taking the train, which takes two hours 22 minutes, as it was the "most effective use of his time".
He said: "The transport the prime minister takes will vary and is always done with any interests of most effective use of 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's most appropriate."
The Green Party said Mr Sunak flying to Leeds is "an unnecessary cost both to the taxpayer and the climate".
Adrian Ramsay, co-leader of the Green Party, told Sky News: "Private jets are estimated to be between five and 14 times more polluting than commercial flights and 50 times more polluting than taking a train.
"It is completely indefensible for Conservative ministers to make such short distance journeys by private jet when a far cheaper and much less damaging option is available."
Labour's deputy leader Angela Rayner added: "Families will be rightly angered by this show of extravagance by Rishi Sunak.
"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."
Johnson/Truss plane controversy
The RAF purchased two Dassault Falcon 900s for £80 million last year to carry VIP passengers, including members of the Royal Family and senior members of the government and military.
They are based at RAF Northolt with the No 32 (The Royal) Squadron.
The two business jets became famous a few months ago when Liz Truss and Boris Johnson flew to Balmoral on 6 September - one on each jet - to meet the Queen to tell her he was stepping down and she was taking over.
At one point, more than 20,000 people were monitoring the outgoing prime minister's flight from London to Aberdeen on flight tracking website FlightRadar24.
The pair were criticised for flying - and on separate private planes - when they could have taken the train, which would have saved 166.6kg of carbon dioxide.
In March 2022, Mr Johnson was also criticised for using a different RAF jet, a P-8A Poseidon, for a photoshoot after it was flown 330 miles from a base in Scotland to a base in Lincolnshire where the then-PM was photographed with the jet before it flew back to its base in Lossiemouth, Moray.