The operator has listed several routes potentially earmarked for closure
Irish Rail is warning potential pay rises could force it into bankruptcy - but the National Bus & Rail Union (NBRU) has said workers are "sick to the back teeth" of the company's comments about their finances.
Unions want an extra 3.75% but the transport company has told the Labour Court it is in a 'perilous financial situation', and may need to cut four routes to stay afloat.
Routes in the firing line include Limerick to Ballybrophy and Limerick Junction to Waterford.
Irish Rail say axing them would save around €5m a year
Closing Gorey to Rosslare would save €4.4m, and shutting the Ennis to Athenry would raise €2.8m.
The lines have been listed on a submission to the Labour Court by Iarnród Éireann.
The Irish Independent says it has seen the document.
It is still unclear what exactly will happen but Irish Rail says one thing is certain.
It says forcing it to up its wage bill would result in an 'immediate financial crisis'.
Corporate communications manager with Irish Rail, Barry Kenny, spoke to Newstalk Breakfast.
He says what happens next is up to Government.
"Ultimately it will be a policy decision and not an Iarnród Éireann decision as to the level of funding and as to the network that we're contracted to provide.
"Our position has been that if the two don't match up - if the funding doesn't match up to the actual cost of maintaining the network - then the overall network starts to deteriorate rather than individual routes."
"We will continue to operate the network that we're contracted to provide".
On the issue of demands for a pay increase, Mr Kenny says: "In a situation where we incur further losses, we will be insolvent - our position has been at the Labour Court that any pay increase has to be generated by productivity".
"Funding the network we regard as a separate issue".
Mr Kenny says the company will be engaging with unions at the Workplace Relations Commission (WRC) from next week.
However, NBRU General Secretary Dermot O'Leary this afternoon responded by saying that workers have had no pay rise in more than nine years.
He suggested: "Whilst one could reluctantly accept that this Country was in the economic mire for a number of years, the fact is now that Iarnrod Éireann has passed Celtic Tiger levels in terms of revenue."
"Staff are frankly sick to the back teeth of listening to the jaded, ‘we have no money’ line from management at this Company, whilst at the same time the NTA, who are after all the funding agent for vital public transport services, support the fact that Iarnrod Éireann has been underfunded for years."