Downing Street said the ‘sole reason’ for the flight was to transport the Prime Minister and staff back from Government business.
The Prime Minister and wife Carrie took their children Wilf and Romy to the sea in Porthminster, St Ives, during the weekend visit to the South West.
The visit came ahead of the Tiverton and Honiton by-election in Devon on June 23.
Triggered by the resignation of the Tory MP caught watching porn in the Commons, the defeat in the former stronghold to the Liberal Democrats was a major blow to Mr Johnson.
The Government plane was sent from London to Royal Naval Air Station Culdrose, near Helston, on the morning of Monday June 13, as first reported by the Sunday Mirror.
On the Friday before, Mr Johnson went to the Royal Cornwall Show, where he visited the cattle and sheep tents and spoke to local traders.
Then on the day of the flight, he went to Southern England Farms in Hayle, where he was photographed driving a tractor, trimming a courgette and weighing broccoli.
A No 10 spokesperson said: “All travel decisions are made with consideration for security and time restraints.
“The PM is accompanied on government business by a delegation of staff, which is taken into consideration as part of ensuring taxpayer value for money.
“This was the sole reason for the plane being used to transport the PM and his staff back from this particular visit.”
The use of the jet not only raises questions about environmental issues but also as to how its use was justified under the ministerial code.
“Ministers must ensure that they always make efficient and cost-effective travel arrangements,” the rulebook states.
“Official transport should not normally be used for travel arrangements arising from party or private business, except where this is justified on security grounds.”
Family members are permitted to join ministers on the trips “provided that it is clearly in the public interest”.
The same plane was used for Mr Johnson’s diplomatic visit to Rwanda, Germany and Spain.
During the G7 summit in Schloss Elmau, the Prime Minister and Canada’s Justin Trudeau compared the relative sizes of their jets.
Mr Johnson said he had seen “Canada Force One” on the tarmac and Mr Trudeau joked that the Prime Minister’s plane was bigger.
“Very modest” was how Mr Johnson described his own jet.