The Scottish Government is planning to merge British Transport Police (BTP) operations north of the border with the national police force.
The BTP said it was vital cross-border counter terrorism measures were maintained following the merger.
In a submission to the Scottish Parliament’s justice committee, the force said: “Any perceived vulnerability arising from disjointed protective arrangements could be exploited by those planning an attack.
“It is therefore important for officials to consider how a devolved model could retain the current seamless counter terrorism approach and awareness of the impact any incident may have to other parts of the infrastructure, as well as enable a swift and assured tactical response.”
The force said there was a threat from "lone-actors" using low sophistication, high impact attacks in crowded places including railway carriages and stations.
It highlighted an incident at Leytonstone Tube station in London last year when a knifeman inspired by the group calling itself Islamic State attempted to behead a fellow passenger and the discovery of an explosive device at North Greenwich station earlier this month.
The devolution of BTP function was a recommendation of the Smith Commission.
However, the Scottish Government’s plans to integrate the service with Police Scotland have proved controversial with critics who claim it is another example of imposing centralised control over policing.