Westminster's Scottish Affairs Committee said the proposals showed "a lack of planning''.
Counter-Terror Work 'Will Not Be Put At Risk By Transport Police Integration'
The integration of transport policing into the national force will not put at risk counter-terrorism in Scotland, the Justice Secretary has said.
Michael Matheson told MSPs he is confident that following the change there will be "no doubt'' about the capacity of Police Scotland to deal with terrorist incidents on the railway network.
He was pressed on the issue by Holyrood's Justice Committee in the wake of last week's terror attack at Westminster in which four people were killed.
The Scottish Government's Railway Policing (Scotland) Bill would result in the British Transport Police (BTP) in Scotland being subsumed into Police Scotland.
MSPs have heard concerns about the potential loss of the seamless coverage currently provided across the UK's railways.
Committee convener Margaret Mitchell questioned whether "taking this risk can be justified'' at a time of heightened security, while Labour MSP Mary Fee called for assurances that there would be no break in the flow of information across the border with the removal of a single command structure across the BTP.
Mr Matheson said: "I'm confident that with the integration of railway policing into Police Scotland there will be no doubt about the capacity of Police Scotland to deal with terrorist incidents if they occurred within our railway network.''
The minister said the creation of a single command structure in Scotland would "reinforce'' the ability to share information, and he highlighted that Police Scotland already has access to the UK-wide intelligence network and beyond through Europol and Interpol.
He said: "Right now if there was a significant terrorist threat on the railways in Scotland, BTP would require the support of Police Scotland to be able to deal with that because BTP in Scotland don't have the specialist capacity to be able to deal with that in themselves.
"Off the back of what happened last week in Westminster, Police Scotland are directly engaged in the network across the whole of the UK in assessing that threat and responding to it with their colleagues across the rest of the UK.
"They have direct links into that intelligence network at the present moment and that will continue to be the case. With the integration of railway policing into Police Scotland, what it will do is it will create a single command structure for how we respond to that particular issue.
"The idea that BTP have some sort of preferential access to intelligence in these matters over and above what access Police Scotland have to intelligence on terrorist issues is simply not true.''
Holyrood's Sport Committee has warned the Protection of Vulnerable Groups (PVG) system "may not be preventing unsuitable people from doing regulated work''.
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