The Department for Transport (DfT) decided in 2008 to procure the trains for Thameslink under a Public Finance Initiative (PFI) contract, which covered the design, finance, production, and maintenance of the train fleet. In June 2011, two years after the contract was originally due to be signed, Cross London Trains, a consortium of Siemens, Innisfree and 3i Infrastructure, was selected as preferred bidder for the fleet of 1150 emu cars. However, delays have continued to blight the process and the contract has still not been signed.

The report says the DfT still expects to let a contract shortly which will require Siemens to deliver the first trains by December 2015 and the final sets by 2018. This would require Siemens to deliver the first trains within less than two years and seven months of contract award. Siemens told IRJ recently that it has already invested a considerable sum in design work to ensure it will be ready to start production when the contract is signed.

The NAO says the delay to the rolling stock contract raises questions over whether the DfT underestimated the scale of the work, time, and skills required to negotiate a "complex" PFI deal. It claims that the delays will add logistical complexity to the infrastructure, particularly around accommodating a new train design, and complicates the process of letting the new franchise because of uncertainty over the schedule for rolling stock delivery.

According the NAO, Siemens remains confident the trains can be delivered within the reduced timescale. However the report suggests the problems in procuring the trains could prevent the overall project being completed on time, and notes that the DfT has not fully investigated whether the 2018 deadline can realistically be met with a revised timetable for delivering the new trains. The report says that this evaluation cannot be carried out until a contract has been signed with the supplier.

The NAO also observes that the delays will have a knock-on effect on the electrification of other parts of the network because of the impact on the planned cascade of emus that are due to released by the delivery of the Siemens trains. Additional Electrostar emus have been ordered from Bombardier in order to provide an interim boost in fleet capacity, but the NAO says the additional procurement raises questions over who bears the risk that these trains will still be needed when the Thameslink programme is completed. It also questions the DfT's role in securing trains and managing their deployment.

The report suggests the infrastructure elements of the project have been handled more successfully. So far, the DfT has kept Thameslink within its original budget of £3.55bn (2006 prices), which it agreed with Network Rail in 2007. Phase one was completed on schedule and within budget, despite revisions to plans for Blackfriars and Farringdon stations, and Blackfriars Bridge being worse condition than expected. Phase 2 has been re-planned to ensure the project remains within budget, although changes the redevelopment of London Bridge station mean commercial income from the project has fallen by £900m, bringing the cost-benefit ratio down to 1.4 to 1.