ScotRail has apologised to customers for what it has described as its "unacceptable service".
The rail operator said it had fallen below the standard expected, but warned customers that disruption would be "ongoing for the foreseeable future".
It follows widespread complaints about cancellations, delays and overcrowded carriages.
Those issues prompted
ministers to issue ScotRail with an eight-week improvement order last month.
In a statement published on ScotRail's website, managing director Alex Hynes said: "We are very sorry to ScotRail customers for our unacceptable service in parts of the country recently.
"While our teams work hard every day to deliver the service you demand, the reality is that we've fallen below the standard you expect and deserve."
Mr Hynes repeated previous claims that problems with training drivers and conductors on new trains and routes had led to cancellations on some services.
He also cited the late delivery of trains by suppliers, including Hitachi and Wabtec, and an overtime ban with the RMT union.
He added: "We are working flat out to train conductors and drivers on Scotland's railway so that we can return services to normal. But that will still take several weeks.
"Since 9 December we have trained 60 drivers and conductors, which is good progress, although we know we need to do more.
"But training will still take several weeks, and that means disruption will be ongoing for the foreseeable future."
In December, Transport Secretary Michael Matheson ordered ScotRail to submit a remedial plan outlining how it planned to address performance issues related to services around Edinburgh, Fife and the Borders.
It comes after ScotRail introduced a new timetable on 9 December, which had promised 100 new services and faster trains.
Mr Hynes, who is managing director of ScotRail Alliance - a partnership between Abellio ScotRail and Network Rail - confirmed that the operator would comply with the Scottish government's order.
