Public servants often end up as the meat in the political sandwich in election campaigns. That has never been more true than it is in 2019, even though we're not even yet into a formal campaign.

What makes this year's public servant sandwich a particularly gourmet feast, however, is that the public servants involved are not just senior officials from Treasury or the Department of Finance as they have been in the past, but our most senior national security officials.

Senate estimates hearings yesterday heard extraordinary evidence from ASIO head Duncan Lewis and the powerful Department of Home Affairs head Michael Pezzullo, in which both made it extremely clear how unhappy they were that their organisations had been dragged into the political fray by the selective leaking of classified advice to the Government — advice leaked in a way that favoured the Government's political message on border protection.

The two senior bureaucrats sent clear shots across the bows of our politicians that such leaks were highly damaging to the way they do their jobs, and also that they did not appreciate being dragged into the scuffle.

'We don't deal with political questions'

Home Affairs secretary Michael Pezzullo gave evidence to Senate estimates. ( ABC News: Matt Roberts )

Mr Lewis told an estimates committee on Monday afternoon that "when reporting wrongly attributes advice from ASIO, or our classified advice is leaked, it undermines all that we stand for".

He was referring to leaked ASIO advice published in The Australian which suggested the medical evacuation bill, if passed, would undermine offshore detention.

For his part, Mr Pezzullo had already taken the extraordinary step of calling in the Australian Federal Police to investigate the leaking of advice attributed to Home Affairs and ASIO to The Australian.

This is despite the fact there are few people in Canberra who believe the advice came from anywhere other than the Government.

The Home Affairs Secretary made clear in Monday afternoon's estimates hearing it was the suggestion that the advice reported in The Australian had come from ASIO that had triggered his referral.

Despite these messages, everything the department had to say in estimates has been seen — and continued to be used — in a political way.

A clearly frustrated Mr Pezzullo told Monday's hearing that: "I have no view and I've expressed no view about the attitude taken by different political parties in the Parliament."

"I just look at the laws that the Parliament generates. Who moved the amendment, who decided to vote, whether the legislation is in favour of the Government's direction or against it, is of no concern to me.

"Any interpretation that somehow my department or the agencies within the portfolio or agencies that we consult with have concerns about what the Parliament has done is a political question.

"We don't deal with political questions.

"We just deal with the passage of laws that the Parliament overall brings down, and how we then implement those laws as the laws of the land."

Home Affairs advice delivered before medevac bill amended

Independent MPs Kerryn Phelps (right) and Julia Banks (left) watch the medical evacuations bill pass the Senate. ( ABC News: Nick Haggarty )

A reading of evidence from estimates that extended over more than 10 hours yesterday paints a very different picture of the security implications of last week's debate about legislation on the medical evacuation of asylum seekers than the one generally reported.

A careful reading, particularly of Mr Pezzullo's evidence, brings a few points to the fore.

The first is that the leaked — and subsequently declassified — advice about the implications of changing the law regarding medical evacuations was advice prepared on the basis of amendments to the legislation passed by the Senate in December, not to the amendments under discussion last week.

"Our concern was that the legislation in prospect, as passed by the Senate in December, attached itself not just to people who were ill but to people who doctors in Australia would want to see for assessment," he told estimates.

"So, on a reasonable worst-case basis, you were looking at effectively the closure of regional processing and the transfer of a thousand people en masse.

"That advice — I just want to be clear about the chronology here — was developed by the department, as the world now knows, in mid-December."

What emerges from the Senate estimates committee is that the department regarded these December amendments as "catastrophic" for the border protection regime. But what is also clearly implied in Mr Pezzullo's evidence is that the amendments last week address the security establishment's concerns.

"It is true that significant features, and I'll call it the Senate version, were modified through the bill's passage in the House, but other features remained intact: refusal of treatment, assessment as well as treatment, recommendation by the two doctors is not just to family members but accompanying support members," he said.

"If you aggregate all of those factors, and absolutely acknowledging that the prospectivity of the legislation was knocked out by confining it to the current group, this was a significant material change that shored up the otherwise significant unravelling of [Operation Sovereign Borders (OSB)] that would have occurred had the Senate version of the bill passed, which would have been catastrophic in terms of its effect on OSB."

7.30 sent a series of questions to Mr Pezzullo asking him to confirm our understanding of his evidence.

One of the questions was: "You talk about the difference between the 'black-letter law' of what was passed by the Parliament and the way the changes they may make to the psychology, sentiment and perceptions of Australia's border protection regime. Does this mean that you believe that, in themselves the legislative changes made by the Parliament will have neither a positive nor negative effect on the regime?"

While he did not add to his answer, he did respond by highlighting this section of his answer yesterday in bold: "This was a significant material change that shored up the otherwise significant unravelling of [Operation Sovereign Borders] that would have occurred had the Senate version of the bill passed which would have been catastrophic in terms of its effect on OSB."

Advice 'about appearance, not reality'

People smugglers could interpret changes to border security as a softening of policy, according to Mr Pezzullo. ( Supplied )

What Home Affairs officials now seem concerned about is not the actual black-and-white law, but any perceptions of a softening of resolve by Australia to stop boats arriving.

"Quite apart from the black-letter law — which of course will be observed to the letter, it is the law of the land now — the question that the Government's concerned about is what this reflects in terms of sentiment: what is the shift?" Mr Pezzullo said at one point.

"Regrettably the smugglers, as the Prime Minister and Mr Dutton and others have made clear, don't actually give you conditions of sale and they don't give you terms of conditions when they try to sell you a product.

"So, if the external sentiment appears to be that policy is softening, and the key factor there relates to the fact that people can come here for either treatment or assessment, and that is the key."

Mr Pezzullo was at some pains to make this point clear, voluntarily reiterating it several times during the time.

"Our concern is: This isn't about strictly what's passed the Parliament; it's about what can be messaged or signalled as what's passed the Parliament and, when taken together with other changes, including for instance the rising number of common law transfers that we mentioned earlier, in aggregate there appears to be — and I just want to stress this is about appearances, not reality — a weakening of resolve.

"That's why it's particularly important that the Government, and indeed future governments, indicate that their resolve to maintain OSB is undiminished."

This in turn has implications for understanding the official advice about reopening Christmas Island.

The estimates evidence is that the Government was originally advised to re-open Christmas Island in the wake of the December amendments on the basis that it may prompt a new flood of boat arrivals.

While Mr Pezzullo told estimates that the department still believed it was necessary to re-open Christmas Island, the reason for that advice has changed to a rationale that it is an important signal to potential asylum seekers that Australia's resolve has not softened about stopping boats.

Changes won't spark new boat arrivals

The Government announced the Christmas Island detention centre would be re-opened following the passing of the medevac bill. ( AAP: Lloyd Jones )

Labor senator Murray Watt asked Mr Pezzullo whether it was correct that the advice that the Government should consider reopening Christmas Island was provided for a set of circumstances that are quite different to what has ultimately been agreed to by the Parliament.

Mr Pezzullo told Senator Watt that the original advice was re-examined in the wake of the parliamentary debate last week.

"That advice in the end had to be reconsidered in light of those amendments," he said.

"It remained the view of the department … that because the bill still dealt with not only medical transfers that related to medical conditions that were evident in the diagnosis that the doctors would receive, but also with a requirement to bring people here for assessment, this would potentially signal, looking at future communications through the various networks that are watching very carefully what's happening in Australia, as the effective unravelling of regional processing.

"Whether this is objectively true or not is beside the point. Because of the conflation, or the conjunction — I shouldn't say 'conflation' — of treatment on assessment, it's our judgement that most people will come here."

7.30 emailed Mr Pezzullo asking whether his evidence suggested "that the advice to re-open Christmas Island was originally given after the December amendments, and on the possibility that, if enacted, they would cause a flood of new arrivals and that, while you still believe the facility should be re-opened, it is primarily for the purposed of acting as a deterrent?"

He sent a one word reply: "Yes".

The political significance of his interventions are twofold — the first is that it makes clear the security establishment does not believe the legislative changes, of themselves, will spark a wave of new boat arrivals.

The second is that, just as Mr Lewis and Mr Pezzullo were sending a clear message to the Government to stop using their advice for political purposes, they are sending a message to Labor — as the alternative new government — that as long as they maintain a tough rhetorical and policy line on border protection, there is no reason to believe that Labor in government is a risk to border policy.