Dublin Bus and Bus Éireann have both confirmed financial problems and may have to reduce services.
Minister for Transport Noel Dempsey says both companies are running at a deficit. However, he said he has asked CIÉ to ensure all peak services are protected and that the customer is the central focus.
Speaking on RTÉ Morning Ireland, he said his goal is to increase passenger numbers.
Hundreds of jobs at Dublin Bus and Bus Éireann may be threatened as management and unions meet in the coming days to discuss the financial situations at both companies.
Dublin Bus has confirmed it will outline the findings of a review it has carried out into financial problems and it plans to address these problems to staff and trade unions on Friday.
It is expected that Dublin Bus will propose the withdrawal of 10% of the Dublin Bus fleet which would amount to around 120 buses and could result in the loss of up to 200 jobs.
Bus Éireann has confirmed that it is also due to hold a meeting to discuss the financial situation on Tuesday.
However, spokespeople for both Dublin Bus and Bus Éireann said it would not be appropriate to comment on speculation that the meetings would propose cuts in services or jobs.
Dublin Bus is considering a number of options including the reduction in frequency or the complete withdrawal of buses from some routes.
Last year, CIE reported a €39.5m operating deficit due a drop in demand for its services and increased fuel costs.