The electrification of the Great Western rail line has been described by MPs as a "stark example of how not to run a major project".
The Public Accounts Committee (PAC) said "mismanagement" of the project had left customers "angry and frustrated".
It warns "similar flaws" could impact on planned electrification schemes on Midlands and TransPennine routes.
Network Rail claimed it had "learnt lessons" and major projects no longer start before being "properly scoped".
However, doubts have been expressed that the plan to electrify the London to Cardiff line can be delivered by December 2018 and to a budget of £2.8bn, while the PAC described a £1.2bn increase in costs "in the space of a year" as "staggering and unacceptable".
Among its recommendations it said the DfT and Network Rail should reassess the case for electrification section-by-section and fund schemes "only where worthwhile benefits for passengers could not be achieved otherwise at lower cost".
The committee added Network Rail needed to produce "realistic cost estimates" and have "robust and detailed" plans.
Meg Hillier MP, chair of the PAC, said mismanagement of the Great Western programme has hit taxpayers hard and left many people angry and frustrated.
"This is a stark example of how not to run a major project, from flawed planning at the earliest stage to weak accountability and what remain serious questions about the reasons for embarking on the work in the first place.
"The sums of public money wasted are appalling - not least the £330m additional costs the Department for Transport will have to pay to keep the trains running because of delays to electrification."
Network Rail said the modernisation was agreed in 2009, "long before the scale of the work was properly understood".
"Network Rail and Department for Transport (DfT) have learnt the lessons from the poor early planning of this project," a spokesman said.
"Today we do not take forward major projects until they are properly scoped, properly planned and we have a robust estimate of what the cost will be."