The company, which manages the infrastructure of the UK railway network, is sending 200 people from its Reading headquarters to a conference in Coventry next Friday.
In a memo leaked to a national newspaper, a senior manager said train tickets could cost up to £27,000 so coaches had been booked instead at £12 per person.
Responding to criticism of the decision, Network Rail argues that it had reduced travel costs to around £2,400.
A Network Rail spokesperson said: "Network Rail makes no apologies for getting best value for the British people. Whilst we have no role in setting train fares, we use rail for the overwhelming number of business journeys. Occasionally, if there is a cheaper alternative we will use that."
The company added that discount train travel for staff did not apply to work trips so full fares were charged.
Next week's conference is being held at Network Rail's Westwood Leadership Centre in Coventry, which provides training to managers and supervisors in partnership with the University of Warwick. The £20m facility features 150 overnight rooms and 40 meeting rooms.