Sir Jeremy Heywood seems to be in some trouble again.

This afternoon, the Prime Minister dragged the Cabinet Secretary into the fiasco over the west coast mainline franchise process. Mr Cameron explained that before the scandal erupted last October, he personally asked Sir Jeremy to investigate whether the bidding process was going OK, and got assurances that all was fine.

Then, in October, the new Transport Secretary Patrick McLoughlin suddenly ordered the bid process to be rerun after it was revealed that the Department for Transport had got its maths wrong and not treated Virgin’s bid for the franchise fairly.

This, of course, is the second time a Heywood inquiry ordered by the PM has failed to get to the bottom of things, following Sir Jeremy’s investigation into the Plebgate affair last September.

On that occasion Heywood failed to discover that an email account accusing Andrew Mitchell of calling police “plebs” actually came from a serving police officer, and not a member of the public.

Mr Cameron told MPs today that Heywood was “very apologetic” and “very angry” given his inquiry into the WCML bid, and what subsequently happened. Heywood had made it clear that the whole civil service had to learn lessons from what went wrong.

Cameron told MPs on the Commons Liaison Committee: “I did ask the Cabinet Secretary to investigate and make absolutely sure this was being done fairly and properly. It turns out the assurances that he got were wrong and the assurances he gave me were wrong. So am I happy with what happened? No, I’m absolutely not, this is not acceptable and that is why we had to stop the franchise.

“The Cabinet Secretary is very apologetic about that and he’s very angry about the fact he feels he was let down by the Department for Transport.”

“Where there are problems, you need departments to surface them early. The people involved in this knew there were problems, and they didn’t surface then,” he told the committee.

“If the Prime Minister asks the Cabinet Secretary for assurances about a process, I think in future it’s going to be very important to make sure that when you go to a department and ask for those things, a better piece of work is done to really make sure you’re getting to the bottom of it. Obviously that didn’t happen in this case.”

OK, David Cameron is making it clear that ultimately he blames the Department for Transport, but what’s interesting about his testimony to the committee is that he kept referring to the Cabinet Secretary (though by title, not name).

He could easily have described this series of events without mentioning him at all, or at least not quite so bluntly.

Follow @MichaelLCrick on Twitter.