Fine Gael and Labour ministers set for clash over cuts to Irish Rail services
Mr Kelly, a Labour TD based in Nenagh and the junior minister for public transport, has strongly campaigned to keep rail services for his constituency.
But now the Limerick-Ballybrophy link, to which Nenagh is central, is among those in the frontline of planned service cuts. It is on a National Transport Authority (NTA) shortlist of routes that could be axed to help Irish Rail balance its books.
The transport regulator was last week given details of passenger numbers across a number of services, and will decide next month which will be cut.
An in-depth review of all services across the rail network is also under way, which could result in some lines being closed.
They include Limerick Junction to Waterford, and Limerick to Ballybrophy in Co Laois, which carried a combined 55,000 passengers last year.
Details of the future shape of the network emerged after Mr Varadkar warned that government funding would be cut and diverted to bus services unless the firm reduced costs and got more people travelling by rail.
In contrast, Mr Kelly sought to placate both management and unions at Irish Rail ahead of Labour Court talks on pay cuts next Monday. The junior minister also refused to discuss potential service cuts.
He has strongly campaigned for Nenagh's rail links. But one study of the Limerick-Ballybrophy line in 2012 showed that 73 people per day travelled on these trains, generating revenue of €753.
The NTA is responsible for approving any changes to timetables, and for paying the Public Service Obligation (PSO) from government to subsidise the cost of running loss-making services. Last December, it asked Irish Rail to submit a "range of proposals" to help reduce costs. Options were provided last week.
PSO payments have fallen by €55m since 2009, and the minister has insisted that Irish Rail funding will be diverted to the public bus companies unless it cuts costs and grows revenues.
Mr Varadkar wants 2pc growth in passenger numbers this year across all public transport operators.
Irish Rail said it was engaged in a "full analysis" of all routes.
The €110m Western Rail Corridor between Galway and Limerick could also see a reduction in services. There is also concern that many passenger journeys on lightly used lines are made by people in receipt of the free travel pass, meaning Irish Rail receives no revenue from the trips.
The threat to services comes as the NTA revealed it will spend €900m up to 2018 on public transport. Some €136.8m is earmarked for the rail network, which includes the cost of reopening the Phoenix Park tunnel and station improvements. Another €215.7m will be spent on buses plus €285.5m on the Luas.
A further €246.8m will go on sustainable transport, including the cycle network and safety measures for pedestrians and cyclists.