It follows dozens of trains a day not running over recent weeks, many because of staff training for new services.
This has yet to be completed despite the launch of an expanded timetable ten days ago because two fleets of trains have arrived late.
Politicians vented their anger at the disruption, with Ettrick, Roxburgh and Berwickshire Conservative Rachael Hamilton describing the impact on the Borders Railway as “absolutely unacceptable”.
Edinburgh Western Liberal Democrat Alex Cole-Hamilton said Edinburgh-bound commuters in Dalmeny had been unable to board trains they were so full.
Mr Matheson said he was “extremely disappointed” to be still speaking about the level of cancelled trains.
He said: “ScotRail has sought to reassure me of a plan of action to address the number of cancellations.”
Mr Matheson said this included 139 extra drivers and conductors being recruited and an “intensive training programme” which would continue through the festive period.
He added that “extra expert planning” support was being added by ScotRail, which the firm said was coming from its parent company Abellio.
However, Mr Matheson said there were continuing delays with the additional trains.
Only 31 of 56 brand new Hitachi electric trains, due to have been delivered by the 9 December timetable change, had reached ScotRail, of an eventual total of 70.
In addition, refurbishment of 26 40-year-old InterCity trains would now not be complete until the end of next year - 12 months late - because of problems at overhaul firm Wabtec.
Labour transport spokesman Colin Smyth said ScotRail should be ordered to take remedial action because two previous improvement plans had proved “inadequate” to tackle its poor performance.
Mr Matheson said 60 per cent of delays were caused by faults which were the responsibility of Network Rail, such as to track and signalling.
Bad weather added to yesterday’s disruption, with the Perth-Inverness line closed north of Dunkeld because of high river water levels which risked damaging a bridge.
Earlier, the Glasgow to Ardrossan and Largs lines were closed because of high tides and strong winds affecting a coastal section of track and overhead wires.