Figures showed that staff at the public body - which owns most of the UK’s railway network - bought 985 plane tickets for flights within the UK.
They bought a further 1,622 for international journeys, Freedom of Information data has revealed.
Many of these domestic journeys could have easily been done by rail - outraging green campaigners who pointed out that getting the train is far more environmentally-friendly.
And among the company’s staff, high-flying director Michelle Handforth - who pockets an annual salary of £330,000 - expensed £8,000 worth of domestic flights.
The news emerged as rail commuters battle with rising fees and have to deal with services which are frequently disrupted by industrial action.
In March, fares saw their biggest hike in a decade back when they increased by 5.9 per cent, figures obtained by The Sun showed.
Meanwhile, unions including the RMT and Aslef have brought much of the rail network to a standstill over recent months when they walked out as part of a continued dispute with their employers over pay and conditions.
The body also saw its net debt grow to £59.1 billion from £56.1 billion over the same period as a result.
A Network Rail spokesperson told The Independent that it will “always encourage our people to travel by rail, but flying is permitted where elements like time constraints are considered”.
Despite this, they said that “some 94 per cent of our business travel is by rail”.
The spokesperson added: “We are competing for top people in a tough global market.
“As a public body, with understandable restrictions on salary and rewards compared to the private sector, we have to be innovative and flexible in order to secure the services of great people from across the internationally competitive market, as we have done here.”
In a later statement, they added: “Most of our international flights were taken by our international consultancy arm, Network Rail Consulting.”
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