But the company says it has no intention of selling off the carriages to help its struggling financial situation.
TDs accused it of presiding over a "massive waste of taxpayers' money" and operating a "carriage graveyard".
But Irish Rail insisted that the spare stock "future-proofed" the rail network.
The Dail Public Accounts Committee (PAC) heard that an initial €500m order was put in with Mitsui for 234 railcars.
The cars, worth €2m each, were delivered in four tranches in 2004, 2005, 2007 and 2008, but not all of the last batch were needed because of declining passenger numbers.
They are InterCity carriages which run on all major routes, except Dublin-Cork and Dublin-Belfast. Gerry Murphy, the CEO of the National Transport Authority (NTA), said they are worth €44m.
PAC chairman John McGuinness questioned Mr Murphy about the unused carriages, describing them as a "massive waste of taxpayers' money".
"Then you increase the fares instead of saying there will be no fare increases until you get your house in order.
"I just can't fathom why you can't put a stop to the carry-on. A company in the private sector would be bust if it did that."
CIE was given a €36m bailout by the Government last year, with €30m going to Irish Rail and €5.33m to Dublin Bus.
And late last year, the NTA sanctioned a rise in CIE fares.
Mr Murphy said the NTA commissioned Jacob's Engineering to assess what to do with the carriages.
It recommended long-term storage, which would reduce maintenance costs.
But an Irish Rail spokeswoman said the carriages were 'rotated' and are 'constantly in service'.
"The order was given when the economy was in a different place. When we have a pick-up in demand, we will have the carriages ready to go," she said.
Fine Gael TD Kieran O'Donnell claimed that people had to stand on a two-hour journey between Limerick and Dublin.
He added Irish Rail had to improve its services if it was to attract business customers, describing the food as "third world" and quality of wi-fi and mobile coverage as "appalling".