Transport Minister Keith Brown said it was "not acceptable" for the UK Government not to tell ministers north of the border it was scrapping the deal for the main West Coast rail line.
The Scottish Government minister said the cancellation of the competition to run trains on the West Coast Main Line after significant flaws were found in the franchise process was "absolutely extraordinary". He said the U-turn by the UK Government "leaves so much up in the air".
Sir Richard Branson had mounted a legal challenge to the Department for Transport (DfT) to award a new 13-year franchise for the busy line not to Virgin Trains, but to rival transport company FirstGroup.
The DfT had intended to contest the matter in court and was hoping FirstGroup would take over the London to Scotland route as planned in December. But, in an embarrassing U-turn for the Government, Transport Secretary Patrick McLoughlin said he was cancelling the competition for the running of the West Coast franchise "because of deeply regrettable and completely unacceptable mistakes made by my department in the way it managed the process".
Mr McLoughlin said the DfT would no longer contest the judicial review and had paused all outstanding franchise competitions pending two independent reviews.
Mr Brown told BBC Radio Scotland: "It is absolutely extraordinary and of course it leaves so much up in the air." The West Coast line links Glasgow with London, and he said the Scottish Government had not been informed about the latest decision.
Speaking on the Good Morning Scotland programme, Mr Brown said: "We once again had no advance notice of this, despite the fact we are talking about a line which takes many thousands, millions of people in fact over the course of the franchise, to and from Scotland. So we're obviously having to try to digest the announcement which has been made."
He added: "The UK Government really has to start talking to Scotland, because these are very important services for Scotland and the idea that we find out about these critical developments on the airwaves in the morning is simply not acceptable."
Asked what clarity there was about the future of the West Coast Main Line, Mr Brown said there was "absolutely none", adding it was unclear who would be running the line after December. He also said the situation raised doubts about the franchise for the ScotRail service. The current franchise runs until 2014 and Mr Brown said the DfT "appear to have suspended all franchising".
He said: "We are very concerned about where this leaves us with the ongoing franchise for the ScotRail bid. We're at a very critical stage in that franchising process and yet we are being told today, or at least hearing on the airwaves, that the process is being suspended. Mr Brown insisted: "We cannot wait around to look at a review which takes a number of months. I would like to have early dialogue with the UK Government about how we go forward."