Virgin asked to run troubled West Coast Mainline for another year while Government attempts to clear-up failed rail franchise mess

The news came as it emerged that more than 30 senior civil servants in the Department for Transport had been axed in the run-up to the West Coast Main Line fiasco.

Virgin was today asked to run West Coast Mainline train services for another year while the Government attempts to sort out the mess left by its failed rail franchise process.

The news, announced to the stock exchange this morning, came as it emerged that more than 30 senior civil servants in the Department for Transport, including some with direct responsibility for franchising, had been axed in the run-up to the West Coast Main Line fiasco.

Documents show that dozens of directors in the department were “eliminated” as part of an aggressive cost-cutting programme, while another 400 more junior posts were closed.

Insiders believe that the speed and scale of the staff reductions – alongside cuts in financial consultancy spending and the introduction of a new, “fiendishly complicated” 13-year franchise agreement – led to the mistakes, which are set to cost the taxpayer more than £100m.

All three areas are to form part of the department's two inquiries into what went wrong. Patrick McLoughlin, the Transport Secretary, will update Parliament this afternoon on the investigations into the fiasco.

But in a statement issued this morning he confirmed that Virgin had been given a temporary extension to run the line for between 9 and 13 months while the inquiries establish what went wrong and a competition is run for an interim franchise agreement.

Mr McLoughlin said: “My priority is to fix the problem and the first step is to take urgent action to ensure that on December 9 services continue to run to the same standard and passengers are not affected.

“I believe Virgin remaining as operator for a short period of time is the best way to do this and my officials and I will be working flat out to make this happen.”

The DfT has also paused the ongoing franchise programme including live competitions on Essex Thameside, Great Western and Thameslink and while two independent reviews into what went wrong with the West Coast competition and the wider DfT rail franchise programme.

The inquiries will focus their attention on what Mr McLoughlin has described as “a number of serious mistakes” that were made in the franchising process.

But they are also expected to examine the wider problems in the department, including staff and consultancy cuts. Among the posts abolished in the restructuring programme was the Director of Procurement – whose role was to oversee the franchise agreements. The directors of Rail Strategy and Rail Contracts, both of which would have had a role in the process, were also axed.

Two other senior posts which dealt with finance were lost in the cull, which saw many responsibilities merged and teams shrunk. Hundreds more junior staff lost their jobs.

Kate Mingay, the most senior civil servant suspended for her role in the franchise decision, had previously been head of Corporate Finance in the department but as a result of the restructuring was given additional responsibilities for rail contracts, procurement and commercial services. At the same time, Department for Transport board minutes from 2010 show that senior officials believed they could have some “quick wins” by cutting consultancy spending.

However, they admitted that other cuts in external support would have “some inevitable implications on prioritisation of expert support”.

In the case of the West Coast Main Line, this is thought to have included not hiring external financial consultants to do an external audit of the department's assumptions and calculations in awarding the franchise.

It is understood to be these problems in financial modelling that led to the scrapping of the decision to hand the franchise to FirstGroup ahead of Virgin Trains. One source, with extensive knowledge of the department, told The Independent: “We always thought the cuts would mean something had to give. We didn't know it would be this bad.”

Another said: “The job cuts at the Department for Transport were faster and more brutal than pretty much anywhere else. They have suggested that it was all been successfully achieved. But with what we know now, you would have to question that.”

The Independent understands that the staff cuts and restructuring will form part of the inquiry being carried out by the Centrica chief executive, Sam Laidlaw, and the former strategy chairman at PricewaterhouseCoopers, Ed Smith. Next month, the think tank Institute for Government is due to publish a report on the effect of the restructuring on Whitehall departments. It looks in detail at the Department for Transport, which made a decision to move faster than others in cutting staff.

Louise Ellman, who chairs the House of Commons Transport Select Committee, said her committee would want to investigate whether the department had a capability to deal with the franchise bids, which were said to be so large that the paperwork needed to be transported in vans.

“Cost-cutting is one of the areas of concern that we have,” she said. “We will be looking to see how much pressure this put on the people who had responsibility for the franchising process.”

Stephen Joseph, of the Campaign for Better Transport, added: “What we have heard is that the Government completely changed the nature of the franchise, cut the number of civil servants by one third and then would not allow them to employ external auditors. None of this has been passenger focused, it has all been about the bottom line.”

Labour MP Maria Eagle, the shadow Transport Secretary, said: “It's increasingly evident that ministerial incompetence caused this rail franchise fiasco. It will add insult to injury if £40m and rising of taxpayers' money has gone down the drain because of short-sighted short cuts made by ministers, designed to save money but ending up costing vastly more. This is yet another reason why we need a genuinely independent inquiry.”

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