The defence secretary has ordered an internal inspection of the UK’s military flying training after Sky News revealed the system to generate RAF pilots is in crisis, it can be revealed.

The move by Ben Wallace is an embarrassing blow for Air Chief Marshal Sir Mike Wigston, the head of the Royal Air Force (RAF), a defence source said.

Mr Wallace gave his chief of the air staff the task of fixing the RAF’s problem-plagued flying training pipeline as his only priority more than two and a half years ago.

However, leaked documents exposed by Sky News last Friday showed that nearly 350 trainee pilots – more than half of the total pool of RAF, Royal Navy and army trainee aviators – were in limbo as of May.

They are either holding for a slot on a flying training course to open-up or taking a refresher course.

It can also be revealed that these so-called “holdies” have effectively been warned the leaking of the documents that shed light on their predicament might even worsen their situation rather than improve it.

A message, which has since been seen by Sky News, was distributed widely throughout the RAF, warning against leaking information to the media.

RAF leadership in ‘tailspin’ over leaks

The author of the official-sounding note said they suspected Air Chief Marshal Wigston and the rest of the senior RAF leadership “are in a total tailspin about this”.

“They will feel let down and disappointed,” the note said.

“They will now be less likely to view the student cohort’s predicament favourably, too.

“Would you, in their position. The military is all about trust, if you betray that knowingly by leaking reams of official information (it’s not exactly a small slip-up in a personal post on social media!), then you can expect that betrayal will have consequences.”

A Ministry of Defence spokesperson confirmed Mr Wallace had instigated the internal inspection, known as a Defence Operational Capability (DOC) audit.

“At the direction of the defence secretary, the MOD is conducting an internal audit of flying training, in recognition of continued challenges with the training pipeline.”

The scope of the audit is still being defined, it is understood.

Hundreds of DOC audits taken place in 30 years

The DOC mechanism was set up in 1995 when Malcolm Rifkind was defence secretary.

It is a tool a defence secretary can use to secure what is meant to be impartial analysis on a topic.

The team of personnel that conduct the audit will sit outside the chain of command of whatever is being inspected, giving it more independence.

Some 220 audits of various issues have taken place over the past nearly three decades.

On flying training, the MOD has already acknowledged that there are challenges to the training pipeline and said that the number of pilots being held now is less than in 2019.

The length of the holding time for trainees can vary from months to even years.

The reasons for the delays are multiple, including most recently a fault with the Rolls Royce-made engine on the Hawk aircraft used to train fast jet pilots.

Ukraine war has put pressure on RAF pilots

Demands on the RAF to fly more missions to defend NATO allies in the wake of Russia’s war in Ukraine also put pressure on the small pool of pilots that are qualified to fly operationally and to instruct trainees.

In addition, a sweeping review of defence last year made changes to the types of aircraft needed on the frontline, which has reduced the number of places available for trainee pilots.

More broadly, pilot training has been under chronic strain since the mid-1990s as successive governments repeatedly cut chunks out of the size of the armed forces, including the RAF, and contracted out large parts of the flying training system to industry.

Under pressure from the Treasury to make as many efficiency savings as possible, the RAF then designed its contractor-run flying training pipeline to meet a minimal requirement rather than include spare capacity to be able to absorb shocks if things go wrong.