More than 14,000 people and vehicles have been stopped and searched by British Transport Police in Scotland since July, it has emerged.
Officers said the threat of a terrorist attack remained high
The stop and search powers had rarely been used before the terrorist attack on Glasgow Airport in June.
Of those stopped at train stations, 12% were from ethnic minorities, but BTP said all searches were random.
The authorities said the searches were carried out to make an attack on the railways as difficult as possible.
Officers stopped 9,994 people and searched 4,636 vehicles at train stations across Scotland between 1 July and 14 December.
BTP can stop and search people at random using powers under Section 44 of the Terrorism Act 2000.
By contrast, Scotland's eight police forces have stopped and searched just 84 people and 51 vehicles between them in 2007.
Justice Secretary Kenny MacAskill called for an explanation as to why the BTP figures were so high.
Mr MacAskill said: "It's a genuine cause for concern.
"Scotland is well served by our police who work for, and with, our communities to protect them.
"Whilst we are in difficult times and it is absolutely vital that we protect our communities, we also have to protect civil liberties too.
"I think we need answers from British Transport Police on why these figures are so high - particularly when our eight local constabularies have always been able to react to similar threats and challenges yet only used these special powers on a much smaller scale."
In 2006/07, BTP officers carried out 30,000 stops throughout England, Scotland and Wales.
A BTP spokesman said: "These operations are carried out as a matter of routine to make the railways as difficult a target for terrorist activity as possible.
"We hope that, as well as disrupting and deterring possible terrorist activity, it will also provide visible reassurance to the travelling public that police are being vigilant for their safety.
"The terrorist threat remains high nationally and it is important that the police and public alike remain vigilant against possible terrorist activity."
The figures emerged just days after Mr MacAskill announced that Strathclyde Police would received £1m to help with the costs of dealing with the terrorist attack on Glasgow Airport.
The cash injection follows a request for extra funds to help with the costs involved, including overtime for officers and calling in assistance from other forces.