The Office of Rail Regulation (ORR) ordered the track operator to remedy "systemic weaknesses" in its planning and management of engineering projects following overruns at Rugby, Liverpool Street Station and Shields Junction.
ORR chief executive Bill Emery said: "What happened over the New Year was totally unacceptable for passengers and freight customers, and to train operating companies. The weakness in Network Rail's management of these projects had a serious impact on all of them and on the reputation of the railway.
"It is quite clear from our thorough investigation that Network Rail is failing to manage major engineering work as consistently well as it should. This is due particularly to weaknesses in the company’s planning, risk assessment and site management of projects as well as to failures of communication within the company and with train operators. We have published a draft Order directing them to address these failings and thus reduce the risk of similar events in the future."
Following the delays Network Rail in January committed itself to bringing more overhead line expertise in-house as well as ordering contractors to cut their dependency on agency staff.
This was due to delays on the West Coast Main Line arising after there failed to be enough agency staff supplied by contractor Jarvis to carry out overhead line work in the allotted possession time.
Emery added that Network Rail had accepted that it currently lacks a robust plan to deliver the upgrade work to the West Coast Main Line needed for the December 2008 service improvements.
Network Rail chief executive Iain Coucher said that although he accepted the regulator's findings, his company intended to appeal its fine.
"We are clear that the ORR has said that what happened at the New Year cannot happen again," said Coucher.
"We agree and accept the findings in the report. We will make changes in the way we plan and manage future work on the railways. Clearly the fine is very significant. We will now be making representations to the ORR that this money should be used to deliver additional and concrete benefits for passengers."