It is understood the CIE is proposing to increase its fares by an average of 6% next year.
The company, which runs Irish Rail, Dublin Bus and Bus Eireann, is in talks with the National Transport Authority (NTA) about fare prices for 2013.
The NTA and not the Government have the final say on fare prices.
It comes after the Government this week announced it is to pump more then €36m into CIE to help it deal with its financial difficulties.
Transport Minister Leo Varadkar said he would prefer if the CIE dealt with its budget deficit by making savings within the company, rather then raising fares.
"We've put an extra €36m into CIE. That can't happen again next year," he said.
"The emphasis now has to be on the company, staff and unions agreeing to changes and agreeing to savings that will make CIE sustainable next year."