The National Audit Office (NAO) has lambasted Great Western railway as "a case study in how not to manage a major programme" in a report into the project.
The cost of modernising the railway is currently estimated at £5.58bn - an increase of £2.1bn since 2013, and there are delays to the electrification of the route of at least 18-36 months. These will cost the Department for Transport (DfT) up to £330m and the NAO has said these increases mean the value for money of the programme needs to be reassessed, and the extent of electrification reconsidered.
Amyas Morse, head of the NAO, said: "The modernisation of the route has potential to deliver significant benefits for passengers but this is a case study in how not to manage a major programme."
He added: "The department's failure to plan and manage all the projects which now make up the Great Western Route Modernisation industry programme in a sufficiently joined up way, combined with weaknesses in Network Rail's management of the infrastructure programme, has led to additional costs for the taxpayer."
Since 2015, Morse said the department and Network Rail "have a better grip", but significant challenges to the timetable remained, and there was more to do "to achieve value for money".
Some passengers in the north and west of England may have to wait up to two years longer to see improvements in services, like increased capacity, because of the delays to the programme.
Meg Hillier MP, chair of the Committee of Public Accounts, said:
The Department for Transport and Network Rail's failure to integrate crucial elements of the modernisation into one programme has cost passengers and taxpayers' time and money. I do not understand why it took the department two years from agreeing to buy new trains to produce a business case.
Several interdependent elements were brought together into an integrated programme last year.
Earlier today, it was revealed that rail minister Paul Maynard had said electrification of four routes within the project had been delayed, in a written statement to Parliament.
A spokesperson for Network Rail said: "The project continues to be challenging and complex but we are making good progress this year and there have been great successes in recent months, including upgrading and electrifying the 130-year-old Severn Tunnel, and completing the Hinksey flood alleviation scheme, near Oxford."
The NAO said Network Rail had "a challenging task" to deliver the main benefits from the infrastructure programme within the current schedule and budget.
The Great Western project in numbers:
18-36 months – minimum delays to electrification destinations along the Great Western route, compared to Network Rail's 2014 plan
£1.2bn – the increase in cost of electrification since 2014
£3.21bn – the cost of the wider infrastructure programme (including electrification) which has risen by £2.1bn since 2013
Up to £330m – the DfT's current estimate of the increase in its net costs caused by delays to electrification
21,200 – the DfT's forecast, in 2012, of the increase in passengers at London Paddington per day during the peak period between 2013-14 and 2018-19: an 81 per cent increase