Nearly 10,000 Scots have been searched by transport police since the terror attack on Glasgow Airport in June.
Officers have stopped 9,994 people and searched 4,636 vehicles at train stations across Scotland since July 1 up to Friday December 14.
Of those searched, 12% were from ethnic minorities but British Transport Police (BTP) said that no target profiling took place and all searches were random.
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: “I think the public would be right to look for a clear explanation on why the British Transport Police in Scotland believe they need to use these powers with such regularity. It’s a genuine cause for concern.”
BTP can stop and search people at random using powers under Section 44 of the Terrorism Act 2000.
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.”