The track operator is also facing a £2 million fine over separate shortcomings south of the Border after an investigation by the rail regulator.
The Office of Rail and Road (ORR) found “numerous errors” in its winter timetable in Scotland. The causes included a lack of quality assurance and detailed planning by Network Rail, which helps run and maintain the UK’s rail tracks, tunnels and some key stations.
The ORR said the firm’s performance in respect of passenger services south of the Border on Southern and Govia Thameslink Railway (GTR), as well as and Scotland were “below expectations” and missed punctuality targets in the past year.
Southern and GTR represented a third of punctuality delays and almost half of cancelled and significantly delayed services in England and Wales, it was found.
ORR is proposing a £2m fine, adding that NR has a chance to offer “reparations” to affected passengers instead of paying the financial penalty.
A spokesman for Transport Scotland said: “Last year’s performance levels fell some way below the standards set by the Scottish Government and expected by passengers.
“We note the conclusions of the ORR’s investigation on the reasons behind this and expect all recommendations to be reflected in full within the planning processes established under the new ScotRail Alliance.”
The ORR said it would be closely monitoring the way Network Rail handled timetable changes involved in a major re-development of Queen Street Station in Glasgow.
ORR said it found no systematic weakness in NR’s performance delivery but it added there had been “repeated past errors” on timetabling, lack of liaison with operators and not planning ahead for passengers.
For Southern and GTR, there were “serious weaknesses” in data for new timetables.
The impact of work on Thameslink was “significantly under-estimated”, which led to severe disruption at London Bridge station earlier this year. There were “numerous errors” in Scotland in the December 2014 timetable caused by issues including a lack of quality assurance and detailed planning.
ORR chief executive Richard Price said: “Our investigation has identified important issues that Network Rail, working with operators, needs to address to improve performance for passengers on these routes.
“Our analysis shows that the company needs to develop a much better understanding of the impact of timetabling on the reliability of services and on rail users. These serious issues have caused severe disruption and frustration for passengers.”
Phil Hufton, managing director, network operations, Network Rail, said: “At the start of this year we had a number of problems that caused passengers disruption and frustration and we apologise for this.”