The Chancellor blamed a train cancellation due to industrial action for choosing the carbon-intensive mode of transport.
It comes as train drivers are striking on the start and end dates of the Tory gathering in the city.
Asked whether he flew, as first reported in the Guardian, Mr Hunt told BBC Breakfast: “I took a BA flight because I was told that my train had been cancelled.”
The flight from London Heathrow Airport to Manchester takes around an hour, according to the BA website, while the train takes about two hours and 15 minutes.
On his return journey, the senior Cabinet minister said: “I’ll probably be driving home because I think there’s another train strike on Wednesday.”
Challenged over what his transport choices said about the state of the railways, Mr Hunt said they “need improving” but declined to comment on the fate of HS2.
Speaking to broadcasters on Monday, he repeatedly said it is not the “appropriate time” to announce whether to cut the northern leg of the high-speed rail project.
He told Sky News: “In terms of things like the northern leg of HS2, whatever decision we make, we will take very careful note of the need to have proper economic infrastructure throughout the whole country.
“In terms of this specific decision I’m afraid you will have to wait.
“We will make the announcement at the appropriate time.”
The Prime Minister has faced a backlash from his predecessors, businesses and leaders across the North for wavering over whether HS2 will ever reach Manchester.
Theresa May was the latest former premier to urge Rishi Sunak not to ditch the Birmingham to Manchester leg of the high-speed rail project that was designed to link the North and London.
A drastic cost-cutting exercise could also see it end at Old Oak Common in the capital’s western suburbs rather than reach its centre.
The Government has stressed the need to assess the value for money, with Mr Hunt questioning why delivering HS2 is costing vastly more than similar projects in Europe.
“I need to have an answer why it costs 10 times more to build high speed rail in this country than it does across the Channel in France,” he told LBC radio.
After the Sun reported that the rail project has 167 members of staff working in its public relations department at a cost of £8 million a year, Mr Hunt said some of the spend is “totally unacceptable”.