Transport Minister Keith Brown is demanding an urgent meeting with the UK Government in the wake of the "shambolic" cancellation of the West Coast main line rail franchise award.
It is "not acceptable" that ministers north of the border were not informed of the decision in advance, he said.
The u-turn by the UK Government on the controversial franchise award "leaves so much up in the air", Mr Brown said.
UK Transport Secretary Patrick McLoughlin said that the cancellation of the franchise award was "wholly and squarely" down to a Whitehall fault. The scrapping of the award will cost taxpayers £40 million after the Department for Transport (DfT) decided to award the contract to Aberdeen-based transport firm FirstGroup.
Sir Richard Branson, whose Virgin Rail company provides the Glasgow to London service on the line, has already mounted a legal challenge to the decision, describing the bidding process as "flawed" and "insane".
The DfT intended to contest the matter in court and hoped that FirstGroup would take over the London to Scotland route as planned in December. But Mr McLoughlin pulled the plug on the whole process, saying "unacceptable mistakes" were made by the DfT in the way it managed the franchise bids from FirstGroup, Virgin and two other companies.
Mr Brown said: "I will do everything I can within our current limited powers to help minimise any uncertainty and disruption for them and I urge the Department for Transport to sort out this horrendous mess and do the same. Despite the fact that this franchise provides services to and from Scotland, we were not advised of the findings nor of the fact that they would be announced today and therefore not included in planning how best to protect the interests of Scottish passengers."
Asked what clarity there was about the future of the West Coast main line, Mr Brown said "absolutely none", adding that it is unclear who will be running the line after December: "The most critical factor is that the services continue and some of the uncertainty that has now been created is eliminated."
Labour's shadow Scottish Secretary Margaret Curran also said more clarity is needed about the future of the line, with business leaders too demanding more information.
Liz Cameron, chief executive of Scottish Chambers of Commerce, said that as a "matter of urgency" the UK Government must provide more information: "The fact that the Department for Transport has blundered on this scale is simply not good enough and the cost both to the public purse and to the private sector bidders is unacceptable."