Canberra had a problem. So it fixed it with secrecy.

On a quest to find out why, we discovered a thing or two about some of the most diplomatically sensitive armed operations Australia has waged abroad during the war on terror.

It is a tale of shifting tactics, prickly neighbours and the prevailing view within the defence and intelligence community that against Islamic State's slickly publicised conquests over the internet, inflicting painful defeats in secret battles is considered a potently effective part of Australian strategy.

It also raises questions for a free democracy — how entitled is the public to basic information about the cost and scale of military action conducted in foreign lands in this country's name?

Right there in the budget — sort of

Oddly, the crumbs of Canberra's 'problem' and its 'fix' were scattered in the pages of this year's budget papers.

Hidden in plain sight under a listing of funding for overseas operations was a new entry: "Operation Augury — Philippines."

An Australian and a Filipino soldier provide medical care during an urban combat skills demonstration in Manila. ( Department of Defence: Corporal Kyle Genner )

Above and below Augury were more than $3 billion worth of mostly foreign military operations — "Okra" in Iraq and the Middle East, "Highroad" in Afghanistan and "Manitou" around the Arabian Gulf — familiar names routinely accounted for in the budget every year.

But intriguingly and uniquely for a budget, the costs of "Operation Augury — Philippines" were blacked out for each of the next four years with the letters "nfp" (not for publication) and a footnote explaining that this was "due to national security issues".

Sources familiar with Australia's almost two decades of battling terrorists overseas have described this secretive treatment of Augury as "unusual" — and all the more so because the broad outline of its original mission was once very publicly heralded.

It raised an obvious question: Why did a military operation in the Philippines suddenly go 'dark'?

The Philippines security nightmare

Ask Australia's military top brass or national security coordinators to name their deepest fears for regional security and the answer quickly draws in on the Philippines.

"That's what keeps me awake at night," one senior officer admitted last year.

Government troops fighting insurgents in Marawi City last year. ( Reuters: Romeo Ranoco )

The dread of a "Raqqa in South-East Asia" explains why Australia moved so quickly last year to stiffen the Philippines Defence Forces with land, sea and air support once Islamic State's local offshoot laid siege to the city of Marawi.

By October, Defence Minister Marise Payne had publicly declared the rapid deployment of about 80 military trainers skilled at urban warfare in the Middle East to drill Filipino soldiers in the finer points of close range combat against the heavily armed militia, known locally as "Maute".

In November, Malcolm Turnbull visited barracks in Manila to marvel at the training mission's success.

"Australia and the Philippines are in the same fight", the Prime Minister declared after watching a demonstration clearance of buildings mocked up on a parade ground.

By then, the task group which also comprised RAAF P3 Orion surveillance crews and a small number of highly experienced Navy personnel had been given its name "Operation Augury — Philippines".

But as 2017 drew to a close, Australia had a rethink about the composition and profile of its mission there.

Augury underwent a makeover that transformed it into something far more sensitive.

Malcolm Turnbull speaking to troops while in Manila for a demonstration of the Australian and Filipino military. ( Department of Defence: Corporal Kyle Genner )

The original rotation of soldiers from the Townsville-based 1RAR battalion headed home to be replaced by others from the same regiment.

The first public hint of a change in tactics appears to have come after Christmas when the local Townsville Bulletin newspaper sought a statement from Defence about what should have been an unremarkable troop turnover but was met with a curt response that it does not "discuss ongoing operational matters including the deployment of personnel".

Into the shadows

Now "Operation Augury" was no longer a standard military training and surveillance exercise — it was receding into the shadows.

Marise Payne and her Philippine counterpart Delfin Lorenzana met to discuss the deployment of Australian troops in September. ( AP: Bullit Marquez )

The urban warfare soldiers were still there, but the Defence Media unit's coverage from 2017, complete with video handouts, abruptly stopped.

The mission is not listed on the Defence Department's online stocktake of overseas operations — it never has been.

In early 2018, Defence took a decision to complete Augury's slide into obscurity by extracting its costs from the budget, then in early stages of preparation.

Various explanations have been offered for the switch and also to define the 'problem' Canberra's security community felt it needed to fix as the year began.

One — from figures knowledgeable about the decision — revolves around the obvious sensitivity within the Philippines to foreign troops being based in their country.

Another is about controlling perceptions that Australia might be unduly interventionist in the neighbourhood.

A third is far more tactically calibrated — that if Islamic State outfits do need to be defeated militarily in Australia's near-region, then it is best their fighters know as little as possible about what has been marshalled against them.

Militants in Marawi City were inspired by the Islamic State group. ( Reuters: Romeo Ranoco )

Their argument is that unlike all of the publicly costed military operations Australia has waged in the Middle-East, always in coalition with other countries, to publish the costs of Augury in the Philippines would give direct and unfiltered information to fighters about what is there.

Send in the spies

There is also a similar but alternative explanation offered by a second group of Defence sources who shared it on condition of anonymity.

To them, the sudden secrecy surrounding the Philippines operation was due to the inclusion of "other elements of the Australian Government. Don't forget we have intelligence agencies".

Australia's spy chief Nick Warner meets with Philippines President Rodrigo Duterte. ( Presidential Broadcast Staff: RadioTelevision Malacañang )

The overseas spy agency ASIS neither confirms nor denies its involvement, but as time has passed it is clear that the visit of its then-director-general Nick Warner to the Presidential Palace in Manila in August 2017 was not for an idle chat and "fist pump" photo with Rodrigo Duterte.

That visit has provided a small amount of 'cover' for one senior government figure contacted by the ABC to acknowledge the existence of activities around Mindanao in the southern Philippines.

Australia is not acting alone but in conjunction with the United States in what was explained as a cooperative regional effort by ASEAN countries alarmed by the speed and relative ease with which Islamic State was able to overrun Marawi last year.

With poorly patrolled maritime borders between the Philippines and North Sulawesi, the Australians are aware that trained jihadists, weapons and explosives are being transferred between the Philippines and Indonesia at levels considered dangerous.

Sorry, this video has expired Five suicide bombers, including a woman with children, targeted Sunday Mass congregations in Surabaya.

At different times in the last eight months, Australian naval ships have patrolled the area, as has the US Navy.

The use of family suicide bombers in Surabaya earlier this month has only elevated fears that knowledge and lethal armaments are reaching Indonesia, despite the best efforts of its counter-terrorism forces — in particular Densus 88.

Augury's little-known roving commission

The grey makeover of "Operation Augury — Philippines" is entirely in keeping with the traditions of a military moniker with an untold history in the Middle East.

Were it not for its cryptic inclusion in this year's budget papers, Operation Augury's existence in other parts of the world might have continued to go unnoticed.

Until now Defence has succeeded in smothering most traces of what appears to be a rolling and adaptive vehicle for performing unstated deeds spanning three countries.

Australia's military presence in Afghanistan dates back to 2001. ( Department of Defence: Corporal Ricky Fuller )

Although never listed among the registry of official operations maintained on the Defence website, "Augury" — meaning the art of interpreting omens — has operated in Afghanistan, Jordan and the United Arab Emirates.

In the few public acknowledgements of its existence, one was in a document that needed to be tabled in Parliament in 2014 and is mirrored in the obscure "pay and conditions" section of the sprawling Defence website — it locks in overseas allowances for troops who supported it in deployments to the three countries.

A Defence source recalling Augury's past believed it had a counter-terrorism function in Afghanistan and the Middle East and "was likely to have involved the SAS".

The person suggested that the name had been carried over to the Philippines because "someone must have envisaged the mission there would evolve beyond the original training role".

What's in a name?

But the same person, experienced in national security matters, was at a loss to explain why Defence was now becoming secretive about the size and cost of its role in Australia's near-region.

"If you put it in the budget, you should put dollars on it would be my opinion, because its existence is now public."

Not that some degree of Defence secrecy should come as a shock to Australians — there are legitimate security reasons why servicemen and women are sent to do deeds in foreign places the public will never know about.

Some — typically spies and special forces — sign-up in full knowledge their service will not be acknowledged.

But in all its wars, this nation's resolve to defeat a threat has historically been measured by two vital metrics; the people and the dollars dedicated to the fight.

At all phases of the war on terror, the Australian public could at least monitor with a degree of transparency the rising financial cost and the vast human scale of the military commitment across the globe.

That is why the curious case of the appearing and vanishing "Operation Augury" is odd.

It is a statement that Australia has entered a fight, the cost of which we are told we must not know — and may never know.