Irish Rail has said it will not accommodate reusable cups on Intercity services for health and safety reasons.
The company says the variety in sizes do not allow for them to be used on catering trolleys.
It also said that "tilting a cup while filling it with boiling water at speeds of up to 70 miles per hour would be a safety issue".
However, they are considering introducing their own which could be bought for repeated use.
The Government is proposing to introduce a charge of up to 25 cent on non-reusable cups to tackle plastic waste.
A spokesperson for Irish Rail confirmed that their catering provider would not be able to support the use of the cups on their Intercity services.
He said: "With the plethora of keep cup types, and volumes, and the importance from a staff and customer safety point of view of ensuring that both pouring and sealing on a moving train must be completely safe and robust, our catering provider on Intercity cannot currently support keep cups.
"On Enterprise, our catering provider has introduced a bespoke keep cup which can be used."
He said that the company was seeking options which could lead to the provision of a similar cup on the Intercity services.
On these routes, the sale of hot drinks are tracked by counting the number of cups used and their contents such as tea or coffee.
The spokesperson said that in looking for alternative options to disposable cups, the catering group would need to change their means of tracking sales.
He said: "We recognise customer demand for a more sustainable alternative and hope to be in a position to address this as soon as possible."
Rail customers voiced their anger on social media today in response to Irish Rail's keep cup policy.
Green Party Councillor Hazel Chu said on Twitter that while the safety of employees and passengers safety "is paramount", Irish Rail has "fallen short" in recent times with their green policies.
She said: "Working together on environment is key so if Irish Rail would like support on green policies, happy to help."
Others described the policy as "crazy", "farcical "disgusting" and "bizarre".
A petition has since been launched urging Irish Rail to reconsider the ban on reusable cups.