A public spending watchdog has cast doubt on the Government's ability to deliver the Thameslink project by the 2018 deadline.
Delays in awarding the contract to build new trains for the major upgrade to a key rail route from Bedford to Brighton risk putting the entire project behind schedule and call into question the skills of Whitehall officials to plan complex transport schemes, according to a National Audit Office (NAO) report.
Margaret Hodge, who chairs the Commons Public Accounts Committee, has raised fears that the Department for Transport (DfT), which has come in for criticism for its handling of a number of schemes including the West Coast Main Line franchise collapse, was "doomed to repeat history".
"Despite the department's chequered history in this area, it was encouraging to see that the first phase of the infrastructure project to alter both Blackfriars and Farringdon stations came in on time and under budget," she says.
"The department now has to build the rest of the infrastructure, buy new trains and let the operating franchise.
"Unlike the shambolic HS2 business case, the case for Thameslink is clear: it is consistently among the most crowded routes in London. However, the department will have to balance the demands of delivering this complex project alongside HS2 and Crossrail.
“With only a small team running Thameslink and their most senior person leaving, I am worried that the department is doomed to repeat history and has underestimated the scale of work, time and skills needed to deliver such an important and complex project.
"There has been a three-year delay trying to agree the £1.6bn contract for trains. There is a risk the 2018 completion date will slip if negotiations with Siemens, the train provider, aren't concluded soon.
“I am concerned at this stage in the project, given the lengthy delays, that the department has left itself with little contingency should anything go wrong. It needs to plan ahead and make sure it avoids another West Coast Main Line-style fiasco."
The NAO report found there continues to be a "robust" transport case for investment in the route, worth £3.552bn in 2006 prices, because the Bedford to Brighton crossing through London is one of the capital's most overcrowded services.
A contract for the trains was supposed to have been signed off by March 2010 but the DfT only selected its preferred bidder – a consortium led by Germany's Siemens at the expense of Bombardier Transportation, which builds trains in Derby – in June 2011 and the deal has yet to be finalised.
The knock-on effect could significantly delay or complicate other parts of the project and is partly behind stalled plans to re-let the franchise for the route, according to the NAO.
It also means the DfT is buying trains to meet short-term demand on newly electrified routes elsewhere in the country which may no longer be needed once the upgrade is complete.
According to the NAO report it is not clear whether the programme can still be delivered by 2018.
"The delays raise questions about whether the department underestimated the scale of work, time and skills and capacity it required to negotiate a complex PFI deal," it added.
Amyas Morse, head of the NAO, says: "It's too early in the Thameslink programme to conclude on whether or not it will achieve value for money. That will have to wait until the new service is running. However, there has been good progress in delivering the first stage of the infrastructure part of the programme on time and under budget, which the department now needs to build on.
"Our principal concern is around the delay in agreeing the contract to build new trains which raises questions about the feasibility of delivering the whole programme by 2018."
Rail Maritime and Transport union general secretary Bob Crow said: "The NAO are confirming everything that RMT has said over the past two years about the chaotic mismanagement of the Thameslink upgrade right up to cabinet level.
“Not only has this disgraceful shambles delayed key rail developments but it has also left 10,000 skilled engineering jobs across the East Midlands hanging in the balance."
A DfT spokesman said: "The procurement process for the new Thameslink rolling stock is complex and it is important that we get it absolutely right in order to ensure the best deal for the taxpayer in these challenging financial times. However we are in the final stages of the process and we expect to conclude the deal shortly.
"We have an experienced senior team in place and are confident that we will be able to deliver the remainder of the project on time and on budget."
Shadow Transport Secretary Maria Eagle said: "It is bad enough that ministers decided to build the new Thameslink trains in Germany, but staggering that they can't even be sure they will be delivered on time.
"The Government has had three years to agree this contract and their failure to do so is now putting at risk the planned 2018 delivery date.
"It is unbelievable that these delays will require taxpayers to fund additional trains to meet short-term demand on newly electrified routes elsewhere in the country because the old Thameslink trains will not be freed up for use as soon as expected."