THE warning from the department of transport’s top civil servant could not be more explicit, as he urges ministers to keep those awful Pacer trains.

Scrapping the ‘cattle trucks’ will be “poor value for money” and bring “relatively few benefits”, writes the permanent secretary, in a letter released today (Friday).

Philip Rutnam goes on to remind the Transport Secretary of the “pressure expected on the department’s budget” – Whitehall-speak for massive post-election cuts looming.

And he writes, of the £250m bill: “Whether or not this is affordable will depend on the outcome of the next spending review.” There may be no money left.

It’s a fascinating insight into decision-making, revealed because this ‘Sir Humphrey’ is determined to cover his back and put the minister’s head on the block.

I’ve never seen such a “ministerial direction” before – and it turned out to be the first issued in the five years of this Coalition.

So what has persuaded Patrick McLoughlin, the normally-cautious Transport Secretary, to over-rule his top civil servant so publicly?

I like to think my interview with David Cameron, last November - when the prime minister vowed “Those trains are going!” – has something to do with it.

Before that guarantee, the Dft was preparing to “modify” the Pacers. Transport sources said there was little doubt the order came from No.10, or from the Chancellor next door.

And that’s because the two top Tories are on a mission to create a ‘Northern Powerhouse’, the buzzphrase used repeatedly by George Osborne in the North-East today.

It is impossible to promise a Powerhouse – with better transport at its heart – and force passengers to rattle around in 30-year-old buses on tracks.

Just as interesting is the dropping of plans for above-inflation fare hikes, to remove an alleged big taxpayer subsidy to Northern trains – which Mr Cameron insisted was unavoidable, back in November.

Yes, the election is ten weeks away, but give ministers credit for listening to the protests it provoked. It turned out to be a genuine consultation. Often, they are not.

Finally, many Northern transport schemes – such as light-rail projects – are rejected because they fail Mr Rutnam’s strict ‘benefit-to-cost ratio’, while London schemes clear the bar with ease.

Now, here is Mr McLoughlin publicly ripping up those rules because, as he states, of the “wider issues” of his “vision for economic growth in the North”.

It’s hugely welcome – but will it make it harder to apply those rules in future?