MPs have questioned whether the Thameslink project will be completed on schedule, amid serious concerns about the progress of the project.
In a new report, the public accounts committee said the Department for Transport lacked project management skills but had completed the first phase on budget.
The department made changes to its plans for the franchise very late in the day. Prior to 2013 the department's approach to letting the franchise to operate the new service was not joined up with the rest of the Thameslink programme, highlighting weaknesses in the department's programme management capability.
We remain concerned about the department's skills and capacity to complete Thameslink by 2018, alongside its ambitious wider portfolio of programmes and projects.
"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."
A public spending watchdog has cast doubt on the Government's ability to deliver a major upgrade to a key rail route by the 2018 deadline.
Delays in awarding the contract to build new trains for the Thameslink risk putting the entire project behind schedule.
The problems call into question the ability of civil servants to plan complex transport schemes, according to the National Audit Office.
The NAO report found there continues to be a "robust" case for investment in the route because Thameslink 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.