Scotland's justice secretary has expressed deep concern at the number of people and vehicles searched by British Transport Police in Scotland.
More than 14,000 have been stopped and searched at train stations since July.
Kenny MacAskill told BBC Scotland he had anecdotal evidence that people going about their business had been "pulled aside and interrogated".
The authorities said the searches were carried out to make an attack on the railways as difficult as possible.
The stop and search powers had rarely been used before the terrorist attack on Glasgow Airport in June and, of those stopped at railway stations, 12% were from ethnic minorities.
But the transport police, who are the responsibility of the UK government, said all searches were random.
Transport officers stopped 9,994 people and searched 4,636 vehicles at train stations across Scotland between 1 July and 14 December, according to the official figures.
They can do so at random, under anti-terrorism legislation.
By contrast, Scotland's eight police forces have stopped and searched just 84 people and 51 vehicles between them in 2007.
Mr MacAskill told BBC Scotland's Politics Show: "I think you have to get the balance right and it would certainly appear to me that things are out of kilter."
"Whether your forefathers fought at the Battle of Bannockburn or whether they've come from the Indian sub-continent, or south of the border, if you're behaving by the law, you're entitled to be treated with respect - not to be routinely stopped, harassed, and investigated.
The justice secretary went on: "I've certainly had anecdotal evidence, including members of staff, of people going about their work, being pulled aside and interrogated. That seems to me to be unacceptable."
"14,000 searches, not over the space of a year. That was since July. It's a period of approximately four months [and] is something that deeply, deeply troubles me."
Mr MacAskill, who said he was planning to hold a meeting with the British Transport Police, said: "If there is a specific threat to a Scottish railway station - that is something that has not been shared with the Scottish Government or the Scottish police officers.
"I think that British Transport Police have to account for themselves if that is the situation."
The British Transport Police said the checks aimed to disrupt possible terrorist activity and provide visible reassurance to the travelling public.
A spokesman added: "The terrorist threat remains high nationally and it is important that the police and public alike remain vigilant against possible terrorist activity."
In 2006/07, British Transport Police officers carried out 30,000 stops throughout England, Scotland and Wales.