Minister for Transport Leo Varadkar has said there will have to be fare increases and reductions in service at CIÉ.
Speaking on RTÉ's Morning Ireland, Mr Vardakar said the State transport company's losses for last year were not as bad as in 2009, but it still lost €50m.
He said CIÉ provided a good service in many areas, but faced problems including falling passenger numbers, a pension deficit and a reduction in State subsidies.
The Minister said the level of fare increases has not yet been determined.
He said it would depend on how much could be saved in cost cuts and how many more people were encouraged to use public transport.
Yesterday, the Minister appointed new chairpersons to CIÉ and its three constituent companies, Dublin Bus, Bus Éireann and Iarnród Éireann.
Two of those posts were filled by people who had responded to a public advertisement.