Network Rail chief executive Mark Carne told MSPs today he cannot give a "cast-iron guarantee" that a full electric train service would start on the main Edinburgh-Glasgow line in December.
His admission confirms a Scotland on Sunday story, which also revealed the first electric trains would not run until October - nearly a year late.
Mr Carne said delays to the Edinburgh Glasgow Improvement Programme (Egip) were "most regrettable" and they would increase its cost, which is currently estimated by Network Rail as £804 million.
However, he declined to say what the final cost of the project would be because "some of the costs are commercially in dispute".
It has yet to be decided whether Network Rail or its contractors, which include Costain and Morgan Sindall, will have to pay the extra costs.
Mr Carne told the Scottish Parliament's rural affairs and connectivity committee: "We will actually have electric trains in October, and we are confident about that, but all projects have risks associated with them and so am I 90 per cent confident?
"I think we're very confident, but it's not a cast-iron guarantee, and I don't think you'd expect that either because events can occur that we will then need to manage."
The latest setback has seen the need to replace some 300 electrical connectors, which Network Rail revealed had not been used before, after some were found to be faulty and posed a safety risk.
Mr Carne also said it was "unacceptable" that some problems had come to light at the last minute, and agreed there should have been tighter project management.
BACKGROUND: Edinburgh-Glasgow electric trains delayed until October http://www.scotsman.com/news/transport/edinburgh-glasgow-electric-trains-delayed-until-october-1-4474484
The first electric trains - transferred from other lines - should have run on the line via Falkirk last December, before being delayed until May, and now to October.
Brand new Hitachi trains are due to replace them in December, some of which will be seven carriages long compared to a maximum of six at present.
Journeys between the two cities are due to be cut by ten minutes to 42 minutes in December 2018 - so long as electrification work on other lines is complete so slower diesel trains can be removed.
Mr Carne said: "I'm not happy with the way the Egip project has run, the electrification part of it, and we've been drilling into it in some depth to turn it around and to improve it, and I'm encouraged by the progress that the team here are making in Scotland to turn that around.
"I think it's most regrettable that we're having these challenges and these difficulties in the delivery of this project.
"Yes, there are some interim milestones along the way which are moving and that's regrettable, because they will incur some additional cost and difficulty, but we're sticking to our guns to deliver the December 2017 timetable change."