The bus and rail group made a loss of €281 million, down from €285 million in 2012.
State grants to the company rose by €13m to €292m, which meant that CIE ended the year with a surplus of €11m. Each year CIE receives massive taxpayer grants to ensure it can provide transport services across the country.
"2012 was extremely difficult for the CIÉ Group, from a financial perspective," the company's chairman Vivienne Jupp said in the report.
"The cumulative effect of five years of reducing demand for public transport, reductions in Exchequer-funded public service obligation payments, the increased cost of fuel and other economic factors led to a serious cash shortage in the group early in the year," she added,
Revenues at CIE rose to almost €725m, the report shows. The company was granted a price hikes by the National Transport Authority during 2012.
According to the annual report, staff costs dropped by about €40m to €558m. Staff numbers fell by 315 to 10,083.
The company's directors were paid a combined €432,000.