CIE has warned of further cuts as records revealed it was more than €43 million in the red last year before the Government bailed it out.
Annual records show the transport firm, which runs Irish Rail, Dublin Bus and the troubled Bus Eireann, secured an extra €36 million in emergency funding in 2012, on top of €256.8 million already secured in State subsidies.
Bus Eireann - which was recently plagued by a strike that grounded its fleet for two days - recorded a loss of €6.2 million despite getting nearly €37 million in State support.
Vivienne Jupp, CIE chairman, said 2012 had been extremely difficult for the group financially after five years of drops in consumer demand, reductions in exchequer grants and other economic factors.
"The challenges the CIE Group face are still significant," she said.
"Nobody should underestimate the task ahead in ensuring that the CIE Group returns to financial stability.
"However, all stakeholders working together - taking the necessary and at times difficult actions needed - will ensure that we can achieve that stability, for the benefit of customers and communities for whom our public transport services are essential to their daily lives."
Figures show the company reported a surplus of some €11.7 million after the Government bailouts. It also sold €21.7 million in assets and made a return on its pension scheme above what was forecast of almost €19 million.
Irish Rail recorded a deficit of €22.5 million and Dublin Bus was €3.8 million in the red, while CIE Tours International witnessed a 9.3% increase in visitor numbers for the year, making a profit of almost €3 million.
Losses were highest in Bus Eireann, where management are implementing a range of measures in a bid to save €5 million.
The deal, hammered out by industrial relations mediators after a strike by drivers, will see top executives and management take a 6% cut in salaries and fees, making up one fifth of cuts.
Increasing the working week from 36 to 39 hours, cutting annual leave and reducing uncertified sickness allowance for all staff will also raise the cash needed.
However Ms Jupp warned cost reduction programmes across all three operating companies are ongoing, in addition to those already agreed.
"Payroll savings and further efficiencies must be delivered," she added.
An analysis of services is also ongoing to ensure bus and rail services match current demand.
Accounts show the group cut operating costs by €7.3 million and increased revenue by €17 million, while 229.3 million passenger journeys were made across bus and rail services.
However there was a cut in the Government's public service obligation grant of 13 million euro and more than €34 million went out in a redundancy programme that cut staff numbers by 325.
Elsewhere its defined benefit pension schemes were also €492 million in deficit.
Siptu trade union is balloting workers across the group for industrial action against cuts.