The Transport Secretary, Patrick McLoughlin, is expected to announce today what interim arrangements have been agreed for the operation of the West Coast Main Line when Virgin's franchise expires in early December. Whatever the deal – and the likelihood must be an extension of Virgin's mandate until such time as the new franchise has been settled – the cost will be just a fraction of the final price to the taxpayer of this debacle, which has been conservatively estimated at £40m.

Thus far, most culpability for the undoubted mess over the West Coast Main Line franchise has attached to civil servants in the Department for Transport, specifically for the use of faulty models for projecting operating costs and passenger numbers. With three senior officials suspended and a slew of reported apologies, including one from the Permanent Secretary to the former Transport Secretary, nothing has altered the impression that this is where the preponderance of responsibility lies.

As we report today, however, there may be much more to this expensively botched franchising process than incompetent civil servants and faulty models. It turns out that the Department for Transport was subject to some of the most rapid and swingeing staffing cuts of any government department; that a large number of senior officials – including 30 directors – lost their jobs, and that the directors of rail strategy and rail contracts were among those whose posts were abolished. Not only this, but the most senior civil servant to be suspended had been given additional responsibilities, which included rail contracts, procurement and commercial services. Could this have left an ill-advised lack of expertise?

Now, of course, there is room for caution. Civil servants do not generally speak in public, even if they feel unjustly accused, but they have other ways of making their unhappiness known. Nor, with the whole department to an extent impugned, were they likely to take the criticism lying down. It is also true that staff reductions breed resentment even when they may be justified. After all, if the restructuring at the Department for Transport claimed the jobs of 30 directors, it is reasonable to ask why there were so many people ranked director in the first place.

Something similar applies to cuts to outside consultants. If outside expertise is so necessary, what does this say about the calibre and qualifications of civil servants? If there are to be cuts, who should take the first hit?

The bigger question here, though, as it applies to the West Coast Main Line franchise, concerns costs and benefits. For if the mishandling of the first competition ends up costing anything in the region of £40m, the sums saved by job cuts and restructuring in the Department for Transport could start to look small by comparison. Indeed, if, as it appears, the department set about cutting jobs, and especially spending on outside consultants, with a speed not replicated elsewhere, the minister who initiated or endorsed it surely has a case to answer.

This restructuring may or may not have seemed the best strategy at the time. But if a link can be drawn between accelerated cost-cutting and overworked staff or gaps in expertise that may have contributed to the West Coast Main Line debacle, lessons must be drawn from the way in which the cuts were carried out, if not from the cuts themselves. We understand that this will be a key aspect of the independent inquiry into what happened. Everyone, from Sir Richard Branson to ministers and the most junior civil servant, has an interest in what it concludes.